Hi,
Distance restraints are *not* imaged, so you may want to re-image your
restart file before restarting your simulation. You can do this with
cpptraj:
parm MyParm.parm7
trajin MyRestart.rst7
autoimage
trajout MyRestart.imaged.rst7
Hope this helps,
-Dan
On Thu, Jul 21, 2016 at 11:25 AM, Stephan Schott <sschottv.gmail.com> wrote:
> Hi everyone,
> I've been doing some simulations using peptides with restraints to maintain
> certain portions of them in close contact (under 15 A). After running some
> steps, the solute drifted away from the center of the box and crossed the
> boundary, point where the restart file was saved. If I try to resume the
> simulations using this restart file, the energy of the system overflows. It
> seems like pmemd.cuda is calculating the distance before reimaging the
> peptides into the PBC and for what I understand the energy overflow might
> be because of the initial force applied to the restraints.
>
> Last steps previous restart:
>
> 490000 14.317 13.127
> 495000 14.657 12.638
>
> mdout:
>
> NSTEP = 500000 TIME(PS) = 63120.000 TEMP(K) = 296.87 PRESS =
> 3.4
> Etot = -1403.4422 EKtot = 12162.4121 EPtot =
> -13565.8543
> BOND = 3775.2357 ANGLE = 4463.7265 DIHED =
> 1038.5834
> 1-4 NB = 260.9989 1-4 EEL = 3109.1481 VDWAALS =
> -21205.1663
> EELEC = -5021.5981 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EAMD_BOOST = 13.2174
> EKCMT = 2239.7843 VIRIAL = 2213.8098 VOLUME =
> 357970.6199
> Density =
> 1.4595
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
>
> First steps after restart:
>
> 0 87.699 13.441
> 5000 ********* *********
>
> mdout:
>
> NSTEP = 5000 TIME(PS) = 63130.000 TEMP(K) =********* PRESS =
> 3530.0
> Etot = ************** EKtot = ************** EPtot =
> **************
> BOND = ************** ANGLE = 1278347.2734 DIHED =
> 3576.7988
> 1-4 NB = 0.0000 1-4 EEL = 0.0057 VDWAALS =
> 2675072.0058
> EELEC = -8962.2636 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EAMBER (non-restraint) = **************
> EAMD_BOOST = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -6813856.5859 VOLUME =
> 254496265.4588
> Density =
> 0.0021
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
>
> If I turn the restraints off (nmropt = 0), the values return to normality:
>
> NSTEP = 5000 TIME(PS) = 63130.000 TEMP(K) = 302.05 PRESS =
> -92.5
> Etot = -1434.3895 EKtot = 12374.6543 EPtot =
> -13809.0438
> BOND = 3651.2393 ANGLE = 4498.2885 DIHED =
> 840.9080
> 1-4 NB = 248.6111 1-4 EEL = 3125.0652 VDWAALS =
> -21158.0471
> EELEC = -5015.1089 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 2302.6129 VIRIAL = 3019.9984 VOLUME =
> 359042.1902
> Density =
> 1.4552
> ------------------------------------------------------------------------------
>
> This simulations where originally intended to be run in chloroform, and I
> posted a question a few days ago in a previous e-mail (
> http://archive.ambermd.org/201607/0330.html). I have the impression that
> the PBC are also giving problems to the aMD options that involve the
> potential energy as a whole (iamd = 1 or 3), as I checked that in the
> simulations, when the protein crosses the box boundary, the energy
> overflows. May I be right?
> Hopefully someone knows if these are real known problems or, if that's not
> the case, has any suggestion what I might be doing wrong.
> Best regards,
>
> --
> Stephan Schott V.
> Bioquímico / Licenciado en Bioquímica
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 02 2016 - 08:30:02 PDT
