MD stop at different time period without giving any error
Dear All
I am using amber 14 for molecular dynamics simulation that was stopped
without giving any error at 12 ns ,19 ns ,29 ns of different protein ligand
complex . I can't understand what is the reason behind this .In Prod.info
file 0f 12ns is
NSTEP = 5783100 TIME(PS) = 12566.200 TEMP(K) = 300.70 PRESS = -407.9
Etot = -30562.5651 EKtot = 6624.5260 EPtot = -37187.0911
BOND = 235.2200 ANGLE = 552.9646 DIHED = 767.3419
1-4 NB = 231.3599 1-4 EEL = 4520.1681 VDWAALS = 6895.1572
EELEC = -50389.3028 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 2911.0340 VIRIAL = 3844.8154 VOLUME = 106013.5791
Density = 1.0554
Ewald error estimate: 0.2098E-03
------------------------------------------------------------
------------------
| Current Timing Info
| -------------------
| Total steps : 25000000 | Completed : 5783100 | Remaining : 19216900
|
| Average timings for last 100 steps:
| Elapsed(s) = 2.71 Per Step(ms) = 27.07
| ns/day = 6.38 seconds/ns = 13532.80
|
| Average timings for all steps:
| Elapsed(s) = 181035.03 Per Step(ms) = 31.30
| ns/day = 5.52 seconds/ns = 15652.08
|
| Estimated time remaining: 167.1 hours.
and when i restart same simulation using sander mpi it is again stop at
NSTEP = 5436400 TIME(PS) = 11872.800 TEMP(K) = 304.85 PRESS = 102.2
Etot = -30650.5478 EKtot = 6715.9220 EPtot = -37366.4699
BOND = 211.4945 ANGLE = 550.8857 DIHED = 748.7218
1-4 NB = 242.2749 1-4 EEL = 4485.1930 VDWAALS = 7176.5078
EELEC = -50781.5476 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 2916.5980 VIRIAL = 2683.1241 VOLUME = 105849.5973
Density = 1.0570
Ewald error estimate: 0.4595E-03
------------------------------------------------------------
------------------
| Current Timing Info
| -------------------
| Total steps : 25000000 | Completed : 5436400 | Remaining : 19563600
|
| Average timings for last 100 steps:
| Elapsed(s) = 2.71 Per Step(ms) = 27.14
| ns/day = 6.37 seconds/ns = 13568.33
|
| Average timings for all steps:
| Elapsed(s) = 148729.95 Per Step(ms) = 27.36
| ns/day = 6.32 seconds/ns = 13679.08
Every time it is stop in different ns of time while there is no change in
min.in ,heat.in, prod.in input files. i want to know why simulation is stop
different time period. while there is same script is used.I need to restart
a molecular dynamics calculation what should I do now?
Thanks
*Metal ion and protein docking - ResearchGate*. Available from:
https://www.researchgate.net/post/Metal_ion_and_protein_dock
ing#view=57c77a9d217e2035797e3a83 [accessed Sep 1, 2016].
*Thank You and Best Wishes*
--
*Regards*
Garima Singh
Central Institute Of Medicinal And Aromatic Plant
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Thu Sep 01 2016 - 02:00:02 PDT
