AMBER Archive (2004)

Subject: AMBER: Sander

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Mon Aug 09 2004 - 11:24:59 CDT

Dear AMBER Users,
 I am running an MD simulation with nonperiodic
conditions, having added a watercap 30 A in radius.I
have two such similar systems which only differ in
that I have manually added extra water molecules to
one of these.
 When I run MD simulations on these the one without
added water molecules does fine, even though the
tempratures are quite high (in both cases).
 Here is the input file and sample output file

&cntrl
nstlim=100000,dt=0.002,
cut=6,ntb=0,
temp0=298,ntt=4,
irest=1,ntx=5,nmropt=1,
ntr=1,tautp=2.0,
ntf=2, ntc=2,
ntwx=500, ntpr=500, ntwr=5000,
nrespa=1,
&end
&wt type='END'
&end
DISANG=./distfinal.rst
LISTOUT=POUT
group input for restrained atoms
2.0
RES 1 475
END
END
-------------------------------------------------------
Here is the distfinal.rst file

 &rst
  ixpk= 0, nxpk= 0, iat=2709,5992, r1= 1.50, r2= 2.00,
r3= 2.00, r4= 2.50,
      rk2=10.0, rk3=10.0, ir6=1, ialtd=0,
 &end

&rst
  ixpk= 0, nxpk= 0, iat=1214,6115, r1= 1.50, r2= 2.00,
r3= 2.00, r4= 2.50,
      rk2=10.0, rk3=10.0, ir6=1, ialtd=0,
 &end
&rst
  ixpk= 0, nxpk= 0, iat=2311,6113, r1= 1.50, r2= 2.00,
r3= 2.00, r4= 2.50,
      rk2=10.0, rk3=10.0, ir6=1, ialtd=0,
 &end
-----------------------------------------------------
Here is sample output for the system with added water
molecules-

KE Trans = 1.0168 KE Rot = 0.1364 C.O.M.
Vel = 0.005420

   Translational and rotational motion removed

   KE Trans = 0.0000 KE Rot = 0.0000
C.O.M. Vel = 0.000000

 NSTEP = 3000 TIME(PS) = 16.000 TEMP(K) =
353.54 PRESS = 0.0
 Etot = -4652.2477 EKtot = 8277.5039 EPtot
    = -12929.7516
 BOND = 1008.6324 ANGLE = 2826.3619 DIHED
    = 3832.3512
 1-4 NB = 1339.6032 1-4 EEL = 13437.2742
VDWAALS = -1331.8680
 EELEC = -34772.0123 EHBOND = 0.0000
RESTRAINT = 729.9059
 EAMBER (non-restraint) = -13659.6575

------------------------------------------------------------------------------

===============================================================================
                      NMR restraints for step 3000
 Energy (this step): Bond = 0.050 Angle =
0.000 Torsion = 0.000
 Energy (tot. run) : Bond = 0.479 Angle =
0.000 Torsion = 0.000

 DEVIATIONS: Target=(r2+r3)/2
Target = closer of r2/r3
            This step Entire run This
step Entire run
           ave. rms ave. rms ave.
rms ave. rms
 Bond 0.034 0.041 0.099 0.116 0.034
0.041 0.099 0.116
 Angle 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
 Torsion 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
===============================================================================
 Frac coord min, max: 0.172812939 1.00001945
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords
(ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error-
------------------------------------------------------
Restarting the calculation didnt help.
So, I tried setting ntt=4 and so that sander sets new
random velocities for virtually all the 100000 steps
the output looks like this-

NSTEP = 500 TIME(PS) = 11.000 TEMP(K) =
148.98 PRESS = 0.0
 Etot = -2992.0186 EKtot = 3488.1011 EPtot
    = -6480.1197
 BOND = 1215.1409 ANGLE = 3353.5687 DIHED
    = 3889.3866
 1-4 NB = 1399.6169 1-4 EEL = 13499.6211
VDWAALS = -302.8256
 EELEC = -30034.5475 EHBOND = 0.0000
RESTRAINT = 499.9193
 EAMBER (non-restraint) = -6980.0389

------------------------------------------------------------------------------

===============================================================================
                      NMR restraints for step 500
 Energy (this step): Bond = 0.493 Angle =
0.000 Torsion = 0.000
 Energy (tot. run) : Bond = 0.412 Angle =
0.000 Torsion = 0.000

 DEVIATIONS: Target=(r2+r3)/2
Target = closer of r2/r3
            This step Entire run This
step Entire run
           ave. rms ave. rms ave.
rms ave. rms
 Bond 0.128 0.128 0.094 0.107 0.128
0.128 0.094 0.107
 Angle 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
 Torsion 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000
===============================================================================
Setting new random velocities at step 501
Setting new random velocities at step 502
Setting new random velocities at step 503
Setting new random velocities at step 504
Setting new random velocities at step 505
Setting new random velocities at step 506
Setting new random velocities at step 507
Setting new random velocities at step 508
Setting new random velocities at step 509
Setting new random velocities at step 510
Setting new random velocities at step 511
Setting new random velocities at step 512
                   .
                   .
                   .
I looked in to the pdb file there off, there are few
water molecules going out of the system ( they are not
the once which I added)
So my question is, whether using ntt=4 for such a
systems is a correct way to solve the error and if not
 
how is it going to affect the results I get.And also
can I modify extraboxdim in nonper.h, and I dont know

how this too is going to affect my results?

Thanks in advance

Regards
Sachin Patil
---------------
Graduate Student
Dept.of Medicinal and Biological CHemistry
University of Toledo, Toledo
43606

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