Have you checked the other output files?
Just as a few suggestions to go through in search for answers. Firstly, in my experience, running sander/pmemd and sander.MPI/pmemd.MPI sometimes produces somewhat different messages.
Just as a suggestion, check whatever status file (mdout or any other "logfile” generated) for errors, also look at the last entries of any “out” files from sander/pmemd. Also, try switching the method (sander/pmemd and MPI or not) to se if that produces any additional information.
Secondly, open up whatever output is produced in any visualisation software (VMD, Chimera, PyMol or whatever you favourite is) and see if anything you can observe looks “wonky”.
Best regards
// Gustaf
> On 26 Mar 2020, at 00:16, Lenka <Vellryba.seznam.cz> wrote:
>
>
> Hello,
>
>
>
>
>
> I prepared my simulation using CHARMM GUI. The minimization and the first
> two NTV steps go well but during the first NTP steps, the simulation
> terminates suddenly.
>
>
>
>
>
> Looking at the mdout file I dont see any error :
>
>
>
>
> These are the few last steps:
>
>
>
>
>
>
> NSTEP = 163000 TIME(PS) = 3163.000 TEMP(K) = 309.14 PRESS =
> 0.0
> Etot = -173038.5827 EKtot = 78598.3047 EPtot = -
> 251636.8874
> BOND = 5876.2198 ANGLE = 19442.3397 DIHED =
> 22210.1528
> UB = 5901.0825 IMP = 662.9250 CMAP = -
> 691.2554
> 1-4 NB = 4866.5260 1-4 EEL = 10290.6195 VDWAALS =
> 7910.8866
> EELEC = -331884.8171 EHBOND = 0.0000 RESTRAINT =
> 3778.4331
> EAMBER (non-restraint) = -255415.3205
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 1216395.6091
> SURFTEN =
> 0.0000
> Density =
> 0.9828
> ---------------------------------------------------------------------------
> ---
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 60.708
> ============================================================================
> ===
>
> NSTEP = 164000 TIME(PS) = 3164.000 TEMP(K) = 309.38 PRESS =
> 0.0
> Etot = -173071.7386 EKtot = 78660.3438 EPtot = -
> 251732.0823
> BOND = 5930.7026 ANGLE = 19458.1416 DIHED =
> 22202.1639
> UB = 5903.8842 IMP = 710.2011 CMAP = -
> 689.7532
> 1-4 NB = 4891.2780 1-4 EEL = 10343.9162 VDWAALS =
> 8172.6994
> EELEC = -332415.3708 EHBOND = 0.0000 RESTRAINT =
> 3760.0546
> EAMBER (non-restraint) = -255492.1369
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 1215769.1927
> SURFTEN =
> 0.0000
> Density =
> 0.9833
> ---------------------------------------------------------------------------
> ---
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 62.983
> ============================================================================
> ===
>
> NSTEP = 165000 TIME(PS) = 3165.000 TEMP(K) = 311.06 PRESS =
> 0.0
> Etot = -172663.5225 EKtot = 79087.8906 EPtot = -
> 251751.4131
> BOND = 5849.1666 ANGLE = 19526.7779 DIHED =
> 22173.2274
> UB = 5903.8152 IMP = 700.1068 CMAP = -
> 698.7184
> 1-4 NB = 4819.8822 1-4 EEL = 10143.8508 VDWAALS =
> 7730.8252
> EELEC = -331664.8678 EHBOND = 0.0000 RESTRAINT =
> 3764.5209
> EAMBER (non-restraint) = -255515.9340
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 1214586.4519
> SURFTEN =
> 0.0000
> Density =
> 0.9842
> ---------------------------------------------------------------------------
> ---
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 64.245
> ============================================================================
> ===
>
> NSTEP = 166000 TIME(PS) = 3166.000 TEMP(K) = 310.75 PRESS =
> 0.0
> Etot = -172438.8479 EKtot = 79007.9688 EPtot = -
> 251446.8166
> BOND = 6015.6529 ANGLE = 19575.1571 DIHED =
> 22202.0826
> UB = 5994.8094 IMP = 672.6210 CMAP = -
> 700.2761
> 1-4 NB = 4858.1225 1-4 EEL = 10008.1277 VDWAALS =
> 7624.8372
> EELEC = -331526.1027 EHBOND = 0.0000 RESTRAINT =
> 3828.1517
> EAMBER (non-restraint) = -255274.9683
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 1214400.5272
> SURFTEN =
> 0.0000
> Density =
> 0.9844
>
>
>
>
>
>
>
>
>
>
> Can anyone help?
>
>
>
>
> Thank you
>
>
>
>
>
> L.
>
>
>
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Received on Thu Mar 26 2020 - 00:00:02 PDT
