Hi Garima,
sounds to me like you restarted the simulation just fine. You may need
to adapt the number of time steps in your input file in order to get to
the desired final simulation time.s
so if your first simulation ran for 15082000 time steps, your input file
for your restart simulation should have ntslim=25000000-15082000
Hope that helps,
Andy
On 05/04/2017 08:48 AM, Garima Singh wrote:
> Dear Amber users,
>
>
>
>
>
> I am new user of AMBER to do some MD calculations and one of my runs was
> stopped after NSTEP = 15082000 When i restart md which was stop at
> TIME(PS) = 31164.000 while in restart output file it start at NSTEP =
> 1000 TIME(PS) = 31167.000 what should i do for restart after this step
> NSTEP = 15082000 TIME(PS) =31164.000 because when i consider NSTEP
> = 1000 TIME(PS) = 31167.000 this step will complete 25000000 step and
> time period increase more then 50 ns.
>
> I am using this file for restart md
> *mpirun -np 4 sander.MPI -O -i Prod.in -o Prod1.out -p cdal7.prmtop -c
> Prod.rst \-r Prod1.rst -x Prod1.mdcrd -inf Pro*
>
>
>
> In Prod.in file
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Production &cntrl imin=0, ntx=5, irest=1, nstlim=25000000, dt=0.002,
> ntf=2, ntc=2, temp0=300.0, ntpr=1000, ntwx=1000, cut=8.0, ntb=2,
> ntp=1, ntt=1, tautp=1.0, ig=-1, /*
>
>
>
> *Md stop at this step*
>
> NSTEP = 15082000 TIME(PS) = 31164.000 TEMP(K) = 298.58 PRESS =
> 298.3
> Etot = -32858.2594 EKtot = 6996.3337 EPtot =
> -39854.5931
> BOND = 197.1791 ANGLE = 525.5396 DIHED =
> 764.3479
> 1-4 NB = 245.8184 1-4 EEL = 4833.2059 VDWAALS =
> 7675.2453
> EELEC = -54095.9292 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 3144.5490 VIRIAL = 2419.4503 VOLUME =
> 112597.1533
> Density = 1.0575 Ewald error estimate: 0.1903E-03
> -----------------------------------------------------------
> -------------------
> | Current Timing Info
> | -------------------
> | Total steps : 25000000 | Completed : 15082000 | Remaining : 9918000
> |
> | Average timings for last 1000 steps:
> | Elapsed(s) = 69.37 Per Step(ms) = 69.37
> | ns/day = 2.49 seconds/ns = 34685.01
> |
> | Average timings for all steps:
> | Elapsed(s) = 531305.95 Per Step(ms) = 35.23
> | ns/day = 4.91 seconds/ns = 17613.91
> |
> | Estimated time remaining: 97.1 hours.
> -----------------------------------------------------------
> -------------------
>
>
>
> *After restart in output file*
>
>
>
> NSTEP = 1000 TIME(PS) = 31167.000 TEMP(K) = 301.22 PRESS =
> -176.7
> Etot = -32888.6102 EKtot = 7058.1857 EPtot =
> -39946.7960
> BOND = 202.8293 ANGLE = 512.9867 DIHED =
> 754.1454
> 1-4 NB = 251.6292 1-4 EEL = 4866.7504 VDWAALS =
> 7681.7094
> EELEC = -54216.8465 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 3149.1134 VIRIAL = 3581.5059 VOLUME =
> 113323.3978
> Density = 1.0507 Ewald error estimate: 0.2970E-03
>
> *I want to know why the simulation is restart from NSTEP=1000 while it
> should restart NSTEP = 15083000 .What should i do to find the exact steps
> and time when md complete after restart ? *
>
>
> Thanks
>
>
>
> *Regards--*
> Garima Singh
> AcSIR-PhD Fellow
> Biotechnology Division
> 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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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Thu May 04 2017 - 00:30:03 PDT
