AMBER Archive (2007)

Subject: AMBER: Restart from restart file obtained from ptraj with added velocities

From: j j (fantvamp_at_gmail.com)
Date: Thu Mar 01 2007 - 10:17:41 CST

Dear Amber Users,
I'm running a dynamic and some water molecules from the periodic box
became about 1000 Angstroms far away from mi solute molecule.
In the restart file appears the following data as coordinates :
[....]
 278.8871558 25.0079552-155.1080085 129.5921211 -44.7975394-158.9746668
 130.3587226 -44.6333529-158.4254885 129.7464466 -45.6652603-159.3481316
  58.9133223************ -13.5743458 59.3766289************ -13.2441555
  58.8037298************ -14.5100250-247.8082567 -68.2815635 316.0647351
-248.1076098 -69.1259269 315.7275852-247.2584052 -68.5048628 316.8157561
 -19.4864297-416.4271252 299.4660246 -18.5491649-416.3421494 299.6407976
[....]
After generating this restart file with asterisks the dynamic crashs.
I've measured the distances of some water molecules and are about 1000
Angtroms in the
previous restart file (which did not give any problem).
To solve this I used ptraj to center and image the water box and I added the
velocities
from the input restart file used as input for ptraj to get the new one
centered.
Although the dynamics runs with no problem now,
the info from the outmd shows diferences:
E01N2e_TIP6_md1905.outmdcenter: 4. RESULTS
E01N2e_TIP6_md1905.outmdcenter---------------------------------------------------------------------------------
E01N2e_TIP6_md1905.outmdcenter-
E01N2e_TIP6_md1905.outmdcenter-
---------------------------------------------------
E01N2e_TIP6_md1905.outmdcenter- APPROXIMATING switch and d/dx switch using
CUBIC SPLINE INTERPOLATION
E01N2e_TIP6_md1905.outmdcenter- using 5000.0 points per unit in tabled
values
E01N2e_TIP6_md1905.outmdcenter- TESTING RELATIVE ERROR over r ranging from
0.0 to cutoff
E01N2e_TIP6_md1905.outmdcenter-| CHECK switch(x): max rel err = 0.2738E-14
at 2.422500
E01N2e_TIP6_md1905.outmdcenter-| CHECK d/dx switch(x): max rel err =
0.8987E-11 at 2.875760
E01N2e_TIP6_md1905.outmdcenter-
---------------------------------------------------
E01N2e_TIP6_md1905.outmdcenter-| Local SIZE OF NONBOND LIST = 65638
E01N2e_TIP6_md1905.outmdcenter-| TOTAL SIZE OF NONBOND LIST = 272885
E01N2e_TIP6_md1905.outmdcenter-check COM velocity, temp: 0.000000
0.00(Removed)
E01N2e_TIP6_md1905.outmdcenter-check COM velocity, temp: 0.000000
0.00(Removed)
E01N2e_TIP6_md1905.outmdcenter-
E01N2e_TIP6_md1905.outmdcenter- NSTEP = 2000 TIME(PS) = 76142.000
TEMP(K) = 297.00 PRESS = 187.5
E01N2e_TIP6_md1905.outmdcenter- Etot = -3116.1764 EKtot =
790.5629 EPtot = -3906.7394
E01N2e_TIP6_md1905.outmdcenter- BOND = 9.0729 ANGLE =
44.3909 DIHED = 68.1440
E01N2e_TIP6_md1905.outmdcenter- 1-4 NB = 14.9853 1-4 EEL = -
33.4091 VDWAALS = 583.8092
E01N2e_TIP6_md1905.outmdcenter- EELEC = -4593.7326 EHBOND =
0.0000 RESTRAINT = 0.0000
E01N2e_TIP6_md1905.outmdcenter- EKCMT = 377.7181 VIRIAL =
323.2509 VOLUME = 13452.3048
E01N2e_TIP6_md1905.outmdcenter-
Density = 0.9883
E01N2e_TIP6_md1905.outmdcenter- Ewald error estimate: 0.3275E-04
E01N2e_TIP6_md1905.outmdcenter-
------------------------------------------------------------------------------
E01N2e_TIP6_md1905.outmdcenter- 

--
E01N2e_TIP6_md1905.outmdnocent:   4.  RESULTS
E01N2e_TIP6_md1905.outmdnocent---------------------------------------------------------------------------------
E01N2e_TIP6_md1905.outmdnocent-
E01N2e_TIP6_md1905.outmdnocent-
---------------------------------------------------
E01N2e_TIP6_md1905.outmdnocent- APPROXIMATING switch and d/dx switch using
CUBIC SPLINE INTERPOLATION
E01N2e_TIP6_md1905.outmdnocent- using   5000.0 points per unit in tabled
values
E01N2e_TIP6_md1905.outmdnocent- TESTING RELATIVE ERROR over r ranging from
0.0 to cutoff
E01N2e_TIP6_md1905.outmdnocent-| CHECK switch(x): max rel err =   0.2738E-14
at   2.422500
E01N2e_TIP6_md1905.outmdnocent-| CHECK d/dx switch(x): max rel err =
0.8987E-11   at   2.875760
E01N2e_TIP6_md1905.outmdnocent-
---------------------------------------------------
E01N2e_TIP6_md1905.outmdnocent-| Local SIZE OF NONBOND LIST =      69969
E01N2e_TIP6_md1905.outmdnocent-| TOTAL SIZE OF NONBOND LIST =     272885
E01N2e_TIP6_md1905.outmdnocent-check COM velocity, temp:        0.000000
0.00(Removed)
E01N2e_TIP6_md1905.outmdnocent-check COM velocity, temp:        0.000000
0.00(Removed)
E01N2e_TIP6_md1905.outmdnocent-
E01N2e_TIP6_md1905.outmdnocent- NSTEP =     2000   TIME(PS) =   76142.000
TEMP(K) =   295.22  PRESS =  -674.9
E01N2e_TIP6_md1905.outmdnocent- Etot   =     -3123.1437  EKtot   =
785.8325  EPtot      =     -3908.9763
E01N2e_TIP6_md1905.outmdnocent- BOND   =        16.8330  ANGLE   =
47.7972  DIHED      =        68.3470
E01N2e_TIP6_md1905.outmdnocent- 1-4 NB =        11.1173  1-4 EEL =       -
34.5713  VDWAALS    =       541.8217
E01N2e_TIP6_md1905.outmdnocent- EELEC  =     -4560.3211  EHBOND  =
0.0000  RESTRAINT  =         0.0000
E01N2e_TIP6_md1905.outmdnocent- EKCMT  =       378.4846  VIRIAL  =
576.4933  VOLUME     =     13587.8619
E01N2e_TIP6_md1905.outmdnocent-
Density    =         0.9784
E01N2e_TIP6_md1905.outmdnocent- Ewald error estimate:   0.5179E-04
E01N2e_TIP6_md1905.outmdnocent-
------------------------------------------------------------------------------
E01N2e_TIP6_md1905.outmdnocent-

Is this correct or may I have followed a diferent way to restart my
simulation,
Thank you,
Best Regards,
JJ

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