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
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Received on Thu Jul 21 2016 - 10:30:02 PDT
