Thanks for the answer. I just wanted to inform in case there's someone else
doing something similar, that I tried checking what happens if I record the
energies and distances for each step after the restart. Indeed the
restraints seem to be the reason behind the crash. I tried to rerun the
simulations from scratch without iwrap and they seem to work, but I still
have problems with aMD, so I will try a different approach.
0 87.699 13.441
1 87.138 13.435
2 86.049 13.440
3 84.503 13.451
4 82.735 13.463
5 85.084 13.473
6 102.724 13.477
7 120.877 13.478
8 131.878 14.305
9 140.149 15.789
10 163.709 14.445
11 342.876 45.941
12 810.940 76.697
13 1521.141 104.982
14 3001.561 541.302
15 4445.991 1312.547
16 5577.594 1224.020
17 6301.041 1841.825
18 6664.001 2326.988
19 6795.514 3538.346
20 6850.866 5196.436
21 6936.450 7141.626
22 7092.349 9156.939
23 7262.057 11020.975
24 7379.165 14508.390
25 7504.649 17342.770
26 7791.737 19360.905
27 7881.461 20542.956
28 9465.469 20987.552
29 10814.774 21513.903
30 13406.938 23021.755
31 15438.806 23616.929
32 16732.801 23456.758
33 18405.062 22436.485
34 20808.729 20754.465
35 24698.866 19355.236
36 30649.287 18109.251
37 38656.779 16921.022
38 46543.586 15785.564
39 56070.674 14483.062
40 67079.934 13206.785
41 78041.155 12249.814
42 90226.350 12036.762
43 ********* 12619.273
44 ********* 13807.669
45 ********* 13878.531
46 ********* 14076.149
NSTEP = 1 TIME(PS) = 63120.002 TEMP(K) = 301.27 PRESS =
-3.2
Etot = 111676.7391 EKtot = 12342.5986 EPtot =
99334.1404
BOND = 3716.4519 ANGLE = 4484.9953 DIHED =
1043.1111
1-4 NB = 260.7038 1-4 EEL = 3110.0471 VDWAALS =
-21202.6704
EELEC = -5025.5227 EHBOND = 0.0000 RESTRAINT =
112947.0243
EAMBER (non-restraint) = -13612.8839
EKCMT = 2236.2923 VIRIAL = 2261.3821 VOLUME =
357970.6953
Density =
1.4595
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2 TIME(PS) = 63120.004 TEMP(K) = 330.36 PRESS =
-2.7
Etot = 111682.9916 EKtot = 13534.6680 EPtot =
98148.3236
BOND = 3775.5511 ANGLE = 4509.3172 DIHED =
1033.0301
1-4 NB = 259.0032 1-4 EEL = 3111.2765 VDWAALS =
-21197.5479
EELEC = -5028.5369 EHBOND = 0.0000 RESTRAINT =
111686.2303
EAMBER (non-restraint) = -13537.9067
EKCMT = 2238.9780 VIRIAL = 2260.0923 VOLUME =
357970.5597
Density =
1.4595
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 3 TIME(PS) = 63120.006 TEMP(K) = 385.49 PRESS =
30.9
Etot = 111626.9582 EKtot = 15793.0566 EPtot =
95833.9016
BOND = 3760.3076 ANGLE = 4664.6266 DIHED =
1013.8326
1-4 NB = 257.6305 1-4 EEL = 3112.3603 VDWAALS =
-21180.7036
EELEC = -5029.8351 EHBOND = 0.0000 RESTRAINT =
109235.6827
EAMBER (non-restraint) = -13401.7812
EKCMT = 2251.3562 VIRIAL = 2012.2840 VOLUME =
357970.4406
Density =
1.4595
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
2016-07-21 19:25 GMT+02:00 Stephan Schott <sschottv.gmail.com>:
> 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
>
--
Stephan Schott V.
Bioquímico / Licenciado en Bioquímica
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Received on Tue Aug 02 2016 - 07:30:02 PDT
