AMBER Archive (2007)
Subject: Re: AMBER: Restart from restart file obtained from ptraj with added velocities

From: j j (fantvamp_at_gmail.com)
Date: Thu Mar 01 2007 - 11:43:13 CST

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In reply to: Thomas Cheatham III: "Re: AMBER: Restart from restart file obtained from ptraj with added velocities"
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Thank you very much,
Outputs setting iwrap=1 or 0 are identical.
Instead of this, if I use ptraj outputs are quite similar,
very small diferences are in:
Thank you again,

| Local SIZE OF NONBOND LIST =
132993 | | Local SIZE OF NONBOND LIST
= 139230
[...]
Etot = -3121.4271 EKtot = 807.9042 EPtot = -
3929.33 | Etot = -3121.4358 EKtot = 807.9048 EPtot
= -3929.34
[...]
EELEC = -4672.9719 EHBOND = 0.0000 RESTRAINT =
0.00 | EELEC = -4672.9812 EHBOND = 0.0000 RESTRAINT
= 0.00
EKCMT = 390.5610 VIRIAL = 111.0107 VOLUME =
13341.36 | EKCMT = 390.5610 VIRIAL = 110.9993 VOLUME
= 13341.36
[...]
Ewald error estimate: 0.5378E-04
| Ewald error estimate: 0.6028E-04
[...]

E01N2e_TIP6_iwrap_md1905.outmd: iwrap = 1, ntwx = 2000,
ntwv = 0, ntwe = 0
E01N2e_TIP6_iwrap_md1905.outmd- ioutfm = 0, ntwprt = 0,
idecomp = 0, rbornstat= 0
E01N2e_TIP6_iwrap_md1905.outmd-
E01N2e_TIP6_iwrap_md1905.outmd-Potential function:
E01N2e_TIP6_iwrap_md1905.outmd- ntf = 2, ntb = 2,
igb = 0, nsnb = 10
E01N2e_TIP6_iwrap_md1905.outmd- ipol = 0, gbsa = 0,
iesp = 0
E01N2e_TIP6_iwrap_md1905.outmd- dielc = 1.00000, cut = 9.00000,
intdiel = 1.00000
E01N2e_TIP6_iwrap_md1905.outmd- scnb = 2.00000, scee = 1.20000
E01N2e_TIP6_iwrap_md1905.outmd-
E01N2e_TIP6_iwrap_md1905.outmd-Frozen or restrained atoms:
E01N2e_TIP6_iwrap_md1905.outmd- ibelly = 0, ntr = 0
E01N2e_TIP6_iwrap_md1905.outmd-
E01N2e_TIP6_iwrap_md1905.outmd-Molecular dynamics:
E01N2e_TIP6_iwrap_md1905.outmd- nstlim = 40000, nscm = 1000,
nrespa = 1
E01N2e_TIP6_iwrap_md1905.outmd- t = 0.00000, dt = 0.00100,
vlimit = 20.00000
E01N2e_TIP6_iwrap_md1905.outmd-
E01N2e_TIP6_iwrap_md1905.outmd-Berendsen (weak-coupling) temperature
regulation:
E01N2e_TIP6_iwrap_md1905.outmd- temp0 = 300.00000, tempi = 300.00000,
tautp = 1.00000
E01N2e_TIP6_iwrap_md1905.outmd-
E01N2e_TIP6_iwrap_md1905.outmd-Pressure regulation:
E01N2e_TIP6_iwrap_md1905.outmd- ntp = 1

-- E01N2e_TIP6_iwrap_md1905.outmd: 4. RESULTS E01N2e_TIP6_iwrap_md1905.outmd--------------------------------------------------------------------------------- E01N2e_TIP6_iwrap_md1905.outmd- E01N2e_TIP6_iwrap_md1905.outmd- --------------------------------------------------- E01N2e_TIP6_iwrap_md1905.outmd- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION E01N2e_TIP6_iwrap_md1905.outmd- using 5000.0 points per unit in tabled values E01N2e_TIP6_iwrap_md1905.outmd- TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff E01N2e_TIP6_iwrap_md1905.outmd-| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 E01N2e_TIP6_iwrap_md1905.outmd-| CHECK d/dx switch(x): max rel err = 0.8987E-11 at 2.875760 E01N2e_TIP6_iwrap_md1905.outmd- --------------------------------------------------- E01N2e_TIP6_iwrap_md1905.outmd-| Local SIZE OF NONBOND LIST = 139230 E01N2e_TIP6_iwrap_md1905.outmd-| TOTAL SIZE OF NONBOND LIST = 272885 E01N2e_TIP6_iwrap_md1905.outmd- E01N2e_TIP6_iwrap_md1905.outmd- NSTEP = 1 TIME(PS) = 76140.001 TEMP(K) = 303.51 PRESS = 970.5 E01N2e_TIP6_iwrap_md1905.outmd- Etot = -3121.4358 EKtot = 807.9048 EPtot = -3929.3405 E01N2e_TIP6_iwrap_md1905.outmd- BOND = 15.2382 ANGLE = 46.2348 DIHED = 71.7608 E01N2e_TIP6_iwrap_md1905.outmd- 1-4 NB = 16.7463 1-4 EEL = - 32.6464 VDWAALS = 626.3069 E01N2e_TIP6_iwrap_md1905.outmd- EELEC = -4672.9812 EHBOND = 0.0000 RESTRAINT = 0.0000 E01N2e_TIP6_iwrap_md1905.outmd- EKCMT = 390.5610 VIRIAL = 110.9993 VOLUME = 13341.3684 E01N2e_TIP6_iwrap_md1905.outmd- Density = 0.9965 E01N2e_TIP6_iwrap_md1905.outmd- Ewald error estimate: 0.6028E-04 -- E01N2e_TIP6_noiwr_md1905.outmd: iwrap = 0, ntwx = 2000, ntwv = 0, ntwe = 0 E01N2e_TIP6_noiwr_md1905.outmd- ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd-Potential function: E01N2e_TIP6_noiwr_md1905.outmd- ntf = 2, ntb = 2, igb = 0, nsnb = 10 E01N2e_TIP6_noiwr_md1905.outmd- ipol = 0, gbsa = 0, iesp = 0 E01N2e_TIP6_noiwr_md1905.outmd- dielc = 1.00000, cut = 9.00000, intdiel = 1.00000 E01N2e_TIP6_noiwr_md1905.outmd- scnb = 2.00000, scee = 1.20000 E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd-Frozen or restrained atoms: E01N2e_TIP6_noiwr_md1905.outmd- ibelly = 0, ntr = 0 E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd-Molecular dynamics: E01N2e_TIP6_noiwr_md1905.outmd- nstlim = 40000, nscm = 1000, nrespa = 1 E01N2e_TIP6_noiwr_md1905.outmd- t = 0.00000, dt = 0.00100, vlimit = 20.00000 E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd-Berendsen (weak-coupling) temperature regulation: E01N2e_TIP6_noiwr_md1905.outmd- temp0 = 300.00000, tempi = 300.00000, tautp = 1.00000 E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd-Pressure regulation: E01N2e_TIP6_noiwr_md1905.outmd- ntp = 1 -- E01N2e_TIP6_noiwr_md1905.outmd: 4. RESULTS E01N2e_TIP6_noiwr_md1905.outmd--------------------------------------------------------------------------------- E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd- --------------------------------------------------- E01N2e_TIP6_noiwr_md1905.outmd- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION E01N2e_TIP6_noiwr_md1905.outmd- using 5000.0 points per unit in tabled values E01N2e_TIP6_noiwr_md1905.outmd- TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff E01N2e_TIP6_noiwr_md1905.outmd-| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 E01N2e_TIP6_noiwr_md1905.outmd-| CHECK d/dx switch(x): max rel err = 0.8987E-11 at 2.875760 E01N2e_TIP6_noiwr_md1905.outmd- --------------------------------------------------- E01N2e_TIP6_noiwr_md1905.outmd-| Local SIZE OF NONBOND LIST = 139230 E01N2e_TIP6_noiwr_md1905.outmd-| TOTAL SIZE OF NONBOND LIST = 272885 E01N2e_TIP6_noiwr_md1905.outmd- E01N2e_TIP6_noiwr_md1905.outmd- NSTEP = 1 TIME(PS) = 76140.001 TEMP(K) = 303.51 PRESS = 970.5 E01N2e_TIP6_noiwr_md1905.outmd- Etot = -3121.4358 EKtot = 807.9048 EPtot = -3929.3405 E01N2e_TIP6_noiwr_md1905.outmd- BOND = 15.2382 ANGLE = 46.2348 DIHED = 71.7608 E01N2e_TIP6_noiwr_md1905.outmd- 1-4 NB = 16.7463 1-4 EEL = - 32.6464 VDWAALS = 626.3069 E01N2e_TIP6_noiwr_md1905.outmd- EELEC = -4672.9812 EHBOND = 0.0000 RESTRAINT = 0.0000 E01N2e_TIP6_noiwr_md1905.outmd- EKCMT = 390.5610 VIRIAL = 110.9993 VOLUME = 13341.3684 E01N2e_TIP6_noiwr_md1905.outmd- Density = 0.9965 E01N2e_TIP6_noiwr_md1905.outmd- Ewald error estimate: 0.6028E-04 -- E01N2e_TIP6_ptraj_md1905.outmd: iwrap = 1, ntwx = 2000, ntwv = 0, ntwe = 0 E01N2e_TIP6_ptraj_md1905.outmd- ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd-Potential function: E01N2e_TIP6_ptraj_md1905.outmd- ntf = 2, ntb = 2, igb = 0, nsnb = 10 E01N2e_TIP6_ptraj_md1905.outmd- ipol = 0, gbsa = 0, iesp = 0 E01N2e_TIP6_ptraj_md1905.outmd- dielc = 1.00000, cut = 9.00000, intdiel = 1.00000 E01N2e_TIP6_ptraj_md1905.outmd- scnb = 2.00000, scee = 1.20000 E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd-Frozen or restrained atoms: E01N2e_TIP6_ptraj_md1905.outmd- ibelly = 0, ntr = 0 E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd-Molecular dynamics: E01N2e_TIP6_ptraj_md1905.outmd- nstlim = 40000, nscm = 1000, nrespa = 1 E01N2e_TIP6_ptraj_md1905.outmd- t = 0.00000, dt = 0.00100, vlimit = 20.00000 E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd-Berendsen (weak-coupling) temperature regulation: E01N2e_TIP6_ptraj_md1905.outmd- temp0 = 300.00000, tempi = 300.00000, tautp = 1.00000 E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd-Pressure regulation: E01N2e_TIP6_ptraj_md1905.outmd- ntp = 1 -- E01N2e_TIP6_ptraj_md1905.outmd: 4. RESULTS E01N2e_TIP6_ptraj_md1905.outmd--------------------------------------------------------------------------------- E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd- --------------------------------------------------- E01N2e_TIP6_ptraj_md1905.outmd- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION E01N2e_TIP6_ptraj_md1905.outmd- using 5000.0 points per unit in tabled values E01N2e_TIP6_ptraj_md1905.outmd- TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff E01N2e_TIP6_ptraj_md1905.outmd-| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 E01N2e_TIP6_ptraj_md1905.outmd-| CHECK d/dx switch(x): max rel err = 0.8987E-11 at 2.875760 E01N2e_TIP6_ptraj_md1905.outmd- --------------------------------------------------- E01N2e_TIP6_ptraj_md1905.outmd-| Local SIZE OF NONBOND LIST = 132993 E01N2e_TIP6_ptraj_md1905.outmd-| TOTAL SIZE OF NONBOND LIST = 272885 E01N2e_TIP6_ptraj_md1905.outmd- E01N2e_TIP6_ptraj_md1905.outmd- NSTEP = 1 TIME(PS) = 76140.001 TEMP(K) = 303.51 PRESS = 970.5 E01N2e_TIP6_ptraj_md1905.outmd- Etot = -3121.4271 EKtot = 807.9042 EPtot = -3929.3313 E01N2e_TIP6_ptraj_md1905.outmd- BOND = 15.2382 ANGLE = 46.2348 DIHED = 71.7608 E01N2e_TIP6_ptraj_md1905.outmd- 1-4 NB = 16.7463 1-4 EEL = - 32.6464 VDWAALS = 626.3069 E01N2e_TIP6_ptraj_md1905.outmd- EELEC = -4672.9719 EHBOND = 0.0000 RESTRAINT = 0.0000 E01N2e_TIP6_ptraj_md1905.outmd- EKCMT = 390.5610 VIRIAL = 111.0107 VOLUME = 13341.3684 E01N2e_TIP6_ptraj_md1905.outmd- Density = 0.9965 E01N2e_TIP6_ptraj_md1905.outmd- Ewald error estimate: 0.5378E-04

2007/3/1, Thomas Cheatham III <tec3_at_utah.edu>: > > > > 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 : > > [....] > > 58.9133223************ -13.5743458 59.3766289************ -13.2441555 > > 58.8037298************ -14.5100250-247.8082567 -68.2815635 316.0647351 > > [....] > > > 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: > > You can also set IWRAP=1 to image the water's, however your approach is > sound, i.e. center/image, write out a new restart file and copy by hand in > the old velocities. Future versions of ptraj will handle the velocities > automagically, that is sometime in the future... > > In spite of this, small differences may result due to finite precision of > the coordinates and box leading to small shifts as it is imaged. The more > box images you are away from the center, the larger the potential > difference. However, it should be small; moreover, from your output it is > not possible to determine where the difference is coming from as you are > showing NSTEP=2000. Given a parallel run and non-determinism in the > communications algorithms, it is not expected that after 2000 steps the > energies will be the same or that the same phase space is sampled. > > What you want to look at is the NSTEP=1 energies and see that these are > close. > > Note that an additional issue can be that ptraj may incorrectly read > restrt or mdcrd files when the numbers munch together as in your example. > A fix is in the works and in the meantime, set IWRAP=1 in the mdin file. > > tec3 @ utah.edu > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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Next message: Raviprasad Aduri: "Re: AMBER: RESP calculation of modified nucleotides"
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In reply to: Thomas Cheatham III: "Re: AMBER: Restart from restart file obtained from ptraj with added velocities"
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AMBER Archive (2007)Subject: Re: AMBER: Restart from restart file obtained from ptraj with added velocities

AMBER Archive (2007)
Subject: Re: AMBER: Restart from restart file obtained from ptraj with added velocities