AMBER Archive (2007)

Subject: AMBER: A question related with periodic boundary condition

From: Jun Liu (junliujun_at_gmail.com)
Date: Wed Sep 19 2007 - 13:42:25 CDT


Dear all,

A follow-up message for the question on the periodic bondary condition.

The command I used is
$sander -O -i nef.in -p nef.top -c nef.xyz -o $output

The input file 'nef.in' for sander is like

============================== ========
   ntt = 0

   temp0 = 29.90, tempi= 29.90,

   dt = 0.0001, nstlim = 11,

   ntwx = 1, ntwv = 1, ntwe = 1, ntb = 1,

   ntpr = 1, cut = 6.11,

   ntx = 1, irest = 0
=======================================

I used tleap to construct "nef.top" and "nef.xyz"
-----------------------------------------------------------------------
nef = loadpdb nef.pdb
set nef box 14.2223
saveamberparm nef nef.top nef.xyz
----------------------------------------------------------------------

nef.xyz is based on a typical FCC(face center cubic) structure of 108 atoms

I checked the force first. I noticed that the forces are very different if a
displacement of every particle in the box was put in the file nef.xyz, i.e,
(x-a, y-a, z-a), where a is the displacement for each particle, i.e. a
translational move of the initial box. However, if the PBC is applied, the
displacement a will not affect the force at all.

For example, the first file "nef.xyz"

   108
   7.1111500 7.1111500 7.1111500 9.4811500 9.4811500 7.1111500
   7.1111500 9.4811500 9.4811500 9.4811500 7.1111500 9.4811500
  11.8521500 7.1111500 7.1111500 14.2221500 9.4811500 7.1111500
  11.8521500 9.4811500 9.4811500 14.2221500 7.1111500 9.4811500
  16.5931500 7.1111500 7.1111500 18.9631500 9.4811500 7.1111500
  16.5931500 9.4811500 9.4811500 18.9631500 7.1111500 9.4811500
   7.1111500 11.8521500 7.1111500 9.4811500 14.2221500 7.1111500
   7.1111500 14.2221500 9.4811500 9.4811500 11.8521500 9.4811500
  11.8521500 11.8521500 7.1111500 14.2221500 14.2221500 7.1111500
  11.8521500 14.2221500 9.4811500 14.2221500 11.8521500 9.4811500
  16.5931500 11.8521500 7.1111500 18.9631500 14.2221500 7.1111500
  16.5931500 14.2221500 9.4811500 18.9631500 11.8521500 9.4811500
   7.1111500 16.5931500 7.1111500 9.4811500 18.9631500 7.1111500
   7.1111500 18.9631500 9.4811500 9.4811500 16.5931500 9.4811500
  11.8521500 16.5931500 7.1111500 14.2221500 18.9631500 7.1111500
  11.8521500 18.9631500 9.4811500 14.2221500 16.5931500 9.4811500
  16.5931500 16.5931500 7.1111500 18.9631500 18.9631500 7.1111500
  16.5931500 18.9631500 9.4811500 18.9631500 16.5931500 9.4811500
   7.1111500 7.1111500 11.8521500 9.4811500 9.4811500 11.8521500
   7.1111500 9.4811500 14.2221500 9.4811500 7.1111500 14.2221500
  11.8521500 7.1111500 11.8521500 14.2221500 9.4811500 11.8521500
  11.8521500 9.4811500 14.2221500 14.2221500 7.1111500 14.2221500
  16.5931500 7.1111500 11.8521500 18.9631500 9.4811500 11.8521500
  16.5931500 9.4811500 14.2221500 18.9631500 7.1111500 14.2221500
   7.1111500 11.8521500 11.8521500 9.4811500 14.2221500 11.8521500
   7.1111500 14.2221500 14.2221500 9.4811500 11.8521500 14.2221500
  11.8521500 11.8521500 11.8521500 14.2221500 14.2221500 11.8521500
  11.8521500 14.2221500 14.2221500 14.2221500 11.8521500 14.2221500
  16.5931500 11.8521500 11.8521500 18.9631500 14.2221500 11.8521500
  16.5931500 14.2221500 14.2221500 18.9631500 11.8521500 14.2221500
   7.1111500 16.5931500 11.8521500 9.4811500 18.9631500 11.8521500
   7.1111500 18.9631500 14.2221500 9.4811500 16.5931500 14.2221500
  11.8521500 16.5931500 11.8521500 14.2221500 18.9631500 11.8521500
  11.8521500 18.9631500 14.2221500 14.2221500 16.5931500 14.2221500
  16.5931500 16.5931500 11.8521500 18.9631500 18.9631500 11.8521500
  16.5931500 18.9631500 14.2221500 18.9631500 16.5931500 14.2221500
   7.1111500 7.1111500 16.5931500 9.4811500 9.4811500 16.5931500
   7.1111500 9.4811500 18.9631500 9.4811500 7.1111500 18.9631500
  11.8521500 7.1111500 16.5931500 14.2221500 9.4811500 16.5931500
  11.8521500 9.4811500 18.9631500 14.2221500 7.1111500 18.9631500
  16.5931500 7.1111500 16.5931500 18.9631500 9.4811500 16.5931500
  16.5931500 9.4811500 18.9631500 18.9631500 7.1111500 18.9631500
   7.1111500 11.8521500 16.5931500 9.4811500 14.2221500 16.5931500
   7.1111500 14.2221500 18.9631500 9.4811500 11.8521500 18.9631500
  11.8521500 11.8521500 16.5931500 14.2221500 14.2221500 16.5931500
  11.8521500 14.2221500 18.9631500 14.2221500 11.8521500 18.9631500
  16.5931500 11.8521500 16.5931500 18.9631500 14.2221500 16.5931500
  16.5931500 14.2221500 18.9631500 18.9631500 11.8521500 18.9631500
   7.1111500 16.5931500 16.5931500 9.4811500 18.9631500 16.5931500
   7.1111500 18.9631500 18.9631500 9.4811500 16.5931500 18.9631500
  11.8521500 16.5931500 16.5931500 14.2221500 18.9631500 16.5931500
  11.8521500 18.9631500 18.9631500 14.2221500 16.5931500 18.9631500

Then the force is

  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  4.264024899510500E-002 0.000000000000000E+000 5.522798184521141E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  2.597452412639459E-003 3.663250348465068E-002 0.134501041258013
  2.976381915174679E-005 0.000000000000000E+000 9.786853777336257E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
 -4.261048517595324E-002 0.000000000000000E+000 5.521620223353677E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 1.260541012453736E-002 8.528080492325615E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  3.729752070572476E-002 5.528691680310158E-002 0.178450536781642
 -9.180185730501808E-002 5.778507560138039E-002 0.134489985488216
 -1.315187272174487E-003 4.524437486800894E-002 -4.393474825249220E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 3.005588155903929E-002 5.521976416664848E-002
  9.184870571818743E-002 3.996696789401211E-002 0.134501041258013
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  1.514451967322923E-002 -0.121836696175586 0.134489985488216
  4.271127049771597E-002 3.729752070572475E-002 0.178450536781642
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  4.262317919052712E-002 0.000000000000000E+000 -4.262317919052712E-002
 -1.526273337669177E-002 -0.147000075331078 0.134489985488216
 -0.134412342480971 -1.526273337669177E-002 0.134489985488216
  0.000000000000000E+000 -8.525108884474261E-002 1.254569522611357E-002
  0.130560972077048 8.790863653722229E-002 6.042275256132802E-002
  0.000000000000000E+000 9.786853777336257E-002 1.260541012453736E-002
  8.528080492325615E-002 0.000000000000000E+000 2.976381915174506E-005
  1.251585095787790E-002 0.000000000000000E+000 1.251585095787790E-002
-3.862339568797764E-002 0.131856679960927 0.105674107166796
  1.774145586756929E-002 0.175822728455908 5.343207116267528E-003
  5.979534750771148E-005 0.000000000000000E+000 -1.251585095787789E-002
 -1.263544165289332E-002 0.000000000000000E+000 1.251585095787790E-002
 -9.179141572662942E-002 0.131861886616876 6.041317447272065E-002
 -1.660514046649756E-002 0.177136995720328 1.529087320207821E-002
 -8.390683972855204E-002 -1.314169847196402E-003 -9.917053309891254E-003
  0.000000000000000E+000 5.516818649770370E-002 5.516818649770370E-002
  0.133170221022241 4.402498345287152E-002 0.104348786493807
  0.000000000000000E+000 5.979534750771148E-005 5.979534750771148E-005
  0.177136269517223 1.642791480625483E-002 1.529232530200243E-002
  2.037190114303933E-002 -1.834036521582133E-002 0.152215653900981
  4.405556963586117E-002 4.668137155240697E-002 0.110878273584300
  2.296918131674231E-002 2.746711062023385E-003 1.795161859752892E-002
  1.194570455533700E-004 2.296845511363747E-002 1.795016649760470E-002
  2.207384484328326E-002 6.430728802820854E-002 0.109587603787609
 -0.177019911216010 5.345389441550844E-003 2.168808487103728E-002
 -2.189151569297228E-002 1.432271712082239E-003 2.746538976501553E-003
 -0.177018265069560 1.905853289597800E-002 2.716946514140312E-003
  0.000000000000000E+000 -9.786853777336257E-002 1.254588248623385E-002
  0.133176444426902 -0.131785814361321 1.645806073454367E-002
 -1.314169847196402E-003 7.398961238655341E-002 2.658512546410426E-003
  0.177136995720328 -1.660514046649755E-002 2.715226896692603E-003
  2.296849354969717E-002 2.470037296293398E-002 6.824880930909788E-002
  8.812143969516746E-005 -0.178332170891123 2.037309070600384E-002
  1.643021624818965E-002 -0.177018316593505 2.716510843933817E-003
  1.432271712082232E-003 -2.189151569297224E-002 2.746538976501581E-003
 -1.926640173515231E-002 -1.926640173515229E-002 2.559574756616718E-002
 -0.133086289221396 -0.137030645559676 1.646099015436769E-002
 -1.792185404964589E-002 -0.178331978024715 8.896629456542349E-005
 -0.177017590256200 -1.660763263827136E-002 2.717963641116733E-003
  0.000000000000000E+000 -4.263152786442490E-002 -5.521976416664848E-002
  0.134501041258013 0.134501041258013 -1.526101395119929E-002
  0.000000000000000E+000 5.521620223353677E-002 -5.519821802605965E-002
  1.314049383369009E-003 -1.313661431210276E-003 -1.520319085475400E-002
  1.254588248623385E-002 0.000000000000000E+000 -9.786853777336257E-002
  8.869877704190579E-005 0.178450536781642 -1.791868152781204E-002
  1.514434751100009E-002 0.131860142967551 -0.139670141932980
  0. -1.260541012453736E-002 0.000000000000000E+000 -9.786853777336257E-002
 -0.134412342480971 0.134489985488216 -1.526273337669176E-002
 -1.394817556666596E-002 0.133175427678191 -0.149628248417061
  4.525253630989801E-002 -4.656755712374162E-002 -1.313374194963909E-003
  0.000000000000000E+000 1.251585095787790E-002 -1.263544165289332E-002
  0.178450536781642 8.869877704191509E-005 -1.791868152781201E-002
  0.000000000000000E+000 -1.254561477702965E-002 -8.522100957574844E-002
  0.133174700777577 1.382978970097428E-002 -0.149629701697103
  2.296866544353827E-002 2.296866544353829E-002 -2.320647091611741E-002
  1.185587569266719E-004 1.185587569266719E-004 -2.320578295739159E-002
  1.774409327737428E-002 2.719153331644630E-003 -0.196180417884048
  8.986554936386143E-005 1.774336637676022E-002 -0.196178964604006
 -2.320647091611745E-002 2.296866544353828E-002 -2.320647091611741E-002
 -0.178331978024715 8.896629456542349E-005 -1.792185404964586E-002
 -1.660656933900602E-002 1.403696266820381E-003 -0.180961604390741
 -0.133086289221396 1.646099015436769E-002 -0.137030645559676
  0.000000000000000E+000 -9.786853777336257E-002 -1.260541012453736E-002
  0.134489985488216 -0.134412342480971 -1.526273337669178E-002
 -8.787491599676585E-002 8.960844358163597E-006 6.740953505176953E-002
  0.133175427678191 -1.394817556666596E-002 -0.137040515566954
  2.296866544353828E-002 -2.320647091611747E-002 -2.320647091611738E-002
  8.896629456542002E-005 -0.178331978024715 -1.792185404964589E-002
  1.514570544372783E-002 -0.134401019193651 -0.134401019193651
  1.403696266820371E-003 -1.660656933900601E-002 -0.180961604390741
 -2.320647091611745E-002 -2.320647091611745E-002 -2.320647091611738E-002
 -0.134401019193651 -0.134401019193651 -1.526445379832693E-002
 -1.526445379832692E-002 -0.134401019193651 -0.134401019193651
 -0.134401019193651 -1.526445379832692E-002 -0.134401019193651
000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000

However, if all coordinates of the particle in "nef.xyz" are shifted by a
displacement ( - 14.222), the force are different.
For example, prepare a second file

"nef.xyz"

   108
  -7.1108500 -7.1108500 -7.1108500 -4.7408500 -4.7408500 -7.1108500
  -7.1108500 -4.7408500 -4.7408500 -4.7408500 -7.1108500 -4.7408500
  -2.3698500 -7.1108500 -7.1108500 0.0001500 -4.7408500 -7.1108500
  -2.3698500 -4.7408500 -4.7408500 0.0001500 -7.1108500 -4.7408500
   2.3711500 -7.1108500 -7.1108500 4.7411500 -4.7408500 -7.1108500
   2.3711500 -4.7408500 -4.7408500 4.7411500 -7.1108500 -4.7408500
  -7.1108500 -2.3698500 -7.1108500 -4.7408500 0.0001500 -7.1108500
  -7.1108500 0.0001500 -4.7408500 -4.7408500 -2.3698500 -4.7408500
  -2.3698500 -2.3698500 -7.1108500 0.0001500 0.0001500 -7.1108500
  -2.3698500 0.0001500 -4.7408500 0.0001500 -2.3698500 -4.7408500
   2.3711500 -2.3698500 -7.1108500 4.7411500 0.0001500 -7.1108500
   2.3711500 0.0001500 -4.7408500 4.7411500 -2.3698500 -4.7408500
  -7.1108500 2.3711500 -7.1108500 -4.7408500 4.7411500 -7.1108500
  -7.1108500 4.7411500 -4.7408500 -4.7408500 2.3711500 -4.7408500
  -2.3698500 2.3711500 -7.1108500 0.0001500 4.7411500 -7.1108500
  -2.3698500 4.7411500 -4.7408500 0.0001500 2.3711500 -4.7408500
   2.3711500 2.3711500 -7.1108500 4.7411500 4.7411500 -7.1108500
   2.3711500 4.7411500 -4.7408500 4.7411500 2.3711500 -4.7408500
  -7.1108500 -7.1108500 -2.3698500 -4.7408500 -4.7408500 -2.3698500
  -7.1108500 -4.7408500 0.0001500 -4.7408500 -7.1108500 0.0001500
  -2.3698500 -7.1108500 -2.3698500 0.0001500 -4.7408500 -2.3698500
  -2.3698500 -4.7408500 0.0001500 0.0001500 -7.1108500 0.0001500
   2.3711500 -7.1108500 -2.3698500 4.7411500 -4.7408500 -2.3698500
   2.3711500 -4.7408500 0.0001500 4.7411500 -7.1108500 0.0001500
  -7.1108500 -2.3698500 -2.3698500 -4.7408500 0.0001500 -2.3698500
  -7.1108500 0.0001500 0.0001500 -4.7408500 -2.3698500 0.0001500
  -2.3698500 -2.3698500 -2.3698500 0.0001500 0.0001500 -2.3698500
  -2.3698500 0.0001500 0.0001500 0.0001500 -2.3698500 0.0001500
   2.3711500 -2.3698500 -2.3698500 4.7411500 0.0001500 -2.3698500
   2.3711500 0.0001500 0.0001500 4.7411500 -2.3698500 0.0001500
  -7.1108500 2.3711500 -2.3698500 -4.7408500 4.7411500 -2.3698500
  -7.1108500 4.7411500 0.0001500 -4.7408500 2.3711500 0.0001500
  -2.3698500 2.3711500 -2.3698500 0.0001500 4.7411500 -2.3698500
  -2.3698500 4.7411500 0.0001500 0.0001500 2.3711500 0.0001500
   2.3711500 2.3711500 -2.3698500 4.7411500 4.7411500 -2.3698500
   2.3711500 4.7411500 0.0001500 4.7411500 2.3711500 0.0001500
  -7.1108500 -7.1108500 2.3711500 -4.7408500 -4.7408500 2.3711500
  -7.1108500 -4.7408500 4.7411500 -4.7408500 -7.1108500 4.7411500
  -2.3698500 -7.1108500 2.3711500 0.0001500 -4.7408500 2.37115
 -2.3698500 -4.7408500 4.7411500 0.0001500 -7.1108500 4.7411500
   2.3711500 -7.1108500 2.3711500 4.7411500 -4.7408500 2.3711500
   2.3711500 -4.7408500 4.7411500 4.7411500 -7.1108500 4.7411500
  -7.1108500 -2.3698500 2.3711500 -4.7408500 0.0001500 2.3711500
  -7.1108500 0.0001500 4.7411500 -4.7408500 -2.3698500 4.7411500
  -2.3698500 -2.3698500 2.3711500 0.0001500 0.0001500 2.3711500
  -2.3698500 0.0001500 4.7411500 0.0001500 -2.3698500 4.7411500
   2.3711500 -2.3698500 2.3711500 4.7411500 0.0001500 2.3711500
   2.3711500 0.0001500 4.7411500 4.7411500 -2.3698500 4.7411500
  -7.1108500 2.3711500 2.3711500 -4.7408500 4.7411500 2.3711500
  -7.1108500 4.7411500 4.7411500 -4.7408500 2.3711500 4.7411500
  -2.3698500 2.3711500 2.3711500 0.0001500 4.7411500 2.3711500
  -2.3698500 4.7411500 4.7411500 0.0001500 2.3711500 4.7411500
   2.3711500 2.3711500 2.3711500 4.7411500 4.7411500 2.3711500
   2.3711500 4.7411500 4.7411500 4.7411500 2.3711500 4.7411500
  14.2223000 14.2223000 14.2223000 90.0000000 90.0000000 90.000000000

and the force is

 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  3.943727428683287E-003 -7.953174555033402E-007 3.942155777904609E-003
 -7.529747735553743E-002 8.659537912072161E-002 1.313712955155562E-003
 -4.265233553982573E-002 8.529289146797682E-002 -4.262257172067401E-002
  5.390515273118551E-002 -3.474468101356645E-002 -3.942591655037865E-003
  1.720855218074070E-007 1.783305984060231E-002 2.628152305096714E-003
 -5.519821802605962E-002 4.266694507431134E-002 3.010740356294839E-006
 -2.657744038726657E-003 0.129247714660547 -4.393628467582957E-002
 -1.651806587490166E-002 1.651879257618296E-002 -1.720855218115269E-007
  0.100426231525989 4.389171440179603E-002 6.699356202162868E-002
  6.623813401143919E-003 -1.265750281414927E-003 -5.266528546649778E-003
  1.783305984060230E-002 -2.598120776740778E-003 -8.523326820599106E-002
 NaN NaN NaN
 NaN NaN NaN
  8.797341275852991E-002 4.138702057219931E-002 0.123892086065810
  0.162141614476140 -4.910959777706507E-002 -9.048974490170629E-002
 NaN NaN NaN
 NaN NaN NaN
 -4.786694744211915E-002 -4.129625713537587E-002 -1.315062581874851E-003
 -0.266724065289845 -4.255078662327165E-002 -9.048884642139889E-002
 NaN NaN NaN
 NaN NaN NaN
 NaN NaN NaN
  0.190915357065759 -4.918109627440796E-002 -3.863696437690001E-002
 NaN NaN NaN
 NaN NaN NaN
 NaN NaN NaN
 NaN NaN NaN
 NaN NaN NaN
 -0.246252018364000 -2.679236932143350E-003 4.786834758309656E-002
 -1.388986771676013E-002 -2.628997346551315E-003 -1.314387768515205E-003
 -0.221437566105834 -1.304859974256604E-003 -8.918819769956010E-002
 -1.520507962102738E-002 1.314439349941148E-003 -1.314439349941148E-003
  1.313712955155564E-003 2.627980219574906E-003 -1.314267264419343E-003
  4.922093924962956E-002 0.105763914256080 -4.659295903005467E-002
 5.912641177998709E-002 -3.998271607406141E-002 -1.314439158260448E-003
  2.985963451478330E-005 0.145685822485755 4.526836425388495E-002
  1.718938411107013E-007 5.254508339225605E-003 -2.627808325733793E-003
  4.790867839439824E-002 0.108391722581813 -5.053503462020780E-002
 NaN NaN NaN
  4.658207720904051E-002 5.913845910086595E-002 2.627808325733792E-003
  1.718938411115686E-007 5.254508339225608E-003 -2.627808325733794E-003
  2.628121562037566E-003 4.659520999763989E-002 -4.922241811879484E-002
 -5.521603033969564E-002 -3.999476339494026E-002 -5.254508339225600E-003
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  8.917696878605214E-002 7.170568967614933E-002 -5.258732353365442E-002
  4.219336377252192E-005 3.406057577294314E-002 -4.922457064872555E-002
  1.388112951157594E-002 8.397023443947285E-002 -2.629433315641767E-003
  0.147079876212523 5.310490186148644E-002 -2.646607594007529E-002
  4.122540837929858E-002 7.297395990049771E-002 -0.101810613363516
 -7.788372370138311E-002 -9.643720309246258E-002 -9.186059669747333E-002
 NaN NaN NaN
 -5.910859866188913E-002 6.436746529317264E-002 -1.520341638674035E-002
 -5.345175626446336E-003 0.120853945156388 -8.795055923654473E-002
 -5.912774437195806E-002 -4.392564409979643E-002 -2.628099057924621E-003
  3.470966971606122E-002 -7.393839793973334E-002 -4.655110945396438E-002
 -5.049463714404170E-002 7.301867623651929E-002 3.822237419695562E-007
  2.628878699882297E-003 -2.646628657647181E-002 -1.314993965700623E-003
 -4.262257172067401E-002 0.000000000000000E+000 -4.264055592815109E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
  4.529723058887185E-002 -0.104466905608814 4.133537291134994E-002
  2.556023036650715E-003 -7.179645308501870E-002 -4.135698901588919E-002
 -8.917696878605219E-002 -4.655439706537811E-002 -4.001167722826884E-002
 -5.286374382928351E-003 -0.150941228615640 4.789689878272362E-002
  1.345407909479221E-003 5.351392638636052E-002 -1.797075429787846E-006
 -3.983886538502991E-003 1.482924416411846E-002 -4.396643071872330E-002
 -4.655439706537812E-002 -4.655439706537812E-002 2.628878699882298E-003
 -3.972107118509076E-003 -0.148313248396066 4.921061173787918E-002
 -4.654258724958148E-002 -0.119676276686115 4.527975389898742E-002
  0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
 NaN NaN NaN
  5.913094740628005E-002 5.918920004272905E-002 2.649052664355174E-003
  5.653025161690571E-002 4.525011627004241E-002 1.313661431210276E-003
 -1.344298792775221E-003 0.100436722645430 1.313712955155564E-003
 NaN NaN NaN
 NaN NaN NaN
 -1.385983618840420E-002 8.786209346702056E-002 1.314387768515207E-003
  1.720855218074070E-007 4.786793793501188E-002 4.523867670489191E-002
 -2.615893674854113E-003 -1.313712955155560E-003 -1.314267264419340E-003
 -2.687167868870591E-003 1.923962639364957E-002 3.962714095565451E-003
 -1.305184830852009E-003 0.143043501615714 4.393394874883293E-002
  0.105694359790114 2.043074494713659E-002 -2.627972476744734E-003
 NaN NaN NaN
  7.038936155993486E-002 -1.123156539366066E-002 -4.130891028946378E-002
 NaN NaN NaN
  4.521271617867728E-002 -2.356445980294886E-002 -8.923317048087667E-002
 NaN NaN NaN
 NaN NaN NaN
 -1.285092495457264E-003 -0.106157168797600 -4.524937439905143E-002
 -5.916787913233541E-002 -2.876225007617970E-002 -5.254890448362689E-003
 -1.388045469821627E-002 0.178463976139159 1.284629677744613E-003
 NaN NaN NaN
 -8.916433149652614E-002 -3.404464382713052E-003 -2.628545985600935E-003
  4.786996980123871E-002 -0.192344698979750 4.919452595012584E-002
  0.000000000000000E+000 -1.257564630538561E-002 0.000000000000000E+000
  1.314272992800467E-003 -7.887428008744403E-003 -1.314272992800467E-003
  5.785680710624087E-002 -9.787003672247420E-002 -4.525060352167490E-002
  1.242481975336249E-003 -7.968961263696621E-002 -4.264076625805201E-002
 -4.129625713537587E-002 -5.781415092475571E-002 1.313712955155560E-003
  1.720855218080575E-007 -3.040870614598789E-002 -2.628152305096710E-003
 -6.173837247274760E-002 -0.189722683984491 -4.525065504562018E-002
 -4.014495212524952E-003 -0.111070532169682 6.551499829494238E-003
 -4.261052439979520E-002 -4.261052439979520E-002 0.000000000000000E+000
  3.441135273244723E-007 -2.308960173652199E-002 -1.031053712260629E-007
 -8.524514344134811E-002 -0.127921667784453 -4.262257172067405E-002

All the interactions between atoms are LJ-interactions. I have checked the
force between two atoms without PBC and it looked fine. Aparently something
is wrong when the PBC is applied.

Could anyone help me with that? Thank you very much!

Best regards
J. L.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu