Are you sure it is stopped? The mdinfo file is written every ntpr steps
I believe, so watch for further updates over the next 167.1 hours it
should run. E.g. you should have some way to see if the process is
running other than by looking at its output, like 'ps' if you are
running it from command line.
Bill
On 3/22/17 11:36 PM, Garima Singh wrote:
> I am using amber 14 for simulation.Why molecular dynamics simulation was
> stopped 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.
>
> I want to know why the simulation is stop . I need to restart a molecular
> dynamics calculation what should I do now? Thanks
>
> *I am using amber 14 for simulation.Why molecular dynamics simulation was
> stopped without giving any error? - ResearchGate*. Available from:
> https://www.researchgate.net/post/I_am_using_amber_14_for_simulationWhy_molecular_dynamics_simulation_was_stopped_without_giving_any_error
> [accessed Mar 23, 2017].
>
> *Thank You and Best Wishes*
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Received on Thu Mar 23 2017 - 01:00:03 PDT
