On Tue, Mar 12, 2013 at 11:35 AM, Attilio Vittorio Vargiu <
attilio.vargiu.gmail.com> wrote:
> Dear Amber users,
> I want to restart and SMD simulation with Amber12.
> Below are the first input file, which I launched with the -O option of
> sander
>
> SMD
> &cntrl
> imin = 0, irest = 0, ntx = 1,
> ntt = 3, gamma_ln = 5.0,
> tempi = 310.0, temp0 = 310.0,
> pres0 = 1.0, ntp = 1, taup = 2.0,
> ntb = 2, ntc = 2, ntf = 2,
> cut = 8, ntr = 0,
> ntpr = 5000, ntwx = 10000, ntwr = 10000, ntwv = 0,
> ioutfm = 1,
> iwrap = 0,
> nstlim = 2000000, dt = 0.002, nrespa = 1, ig = -1,
> jar = 1
> /
> &wt type='DUMPFREQ', istep1=100 /
> &wt type='END' /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LISTOUT=POUT
>
> and here is the restart input file, which I launched with the -A option,
> that should be used in conjunction with irest=1 for restarting simulation
> and appending to existing files:
>
> &cntrl
> imin = 0, *irest = 1, ntx = 5*,
> ntt = 3, gamma_ln = 5.0,
> temp0 = 310.0,
> pres0 = 1.0, ntp = 1, taup = 2.0,
> ntb = 2, ntc = 2, ntf = 2,
> cut = 8, ntr = 0,
> ntpr = 5000, ntwx = 10000, ntwr = 10000, ntwv = 0,
> ioutfm = 1,
> iwrap = 0,
> nstlim = 2000000, dt = 0.002, nrespa = 1,
> jar = 1
> /
> &wt type='DUMPFREQ', istep1=100 /
> &wt type='END' /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LISTOUT=POUT
>
> Now, while the mdinfo and trajectory files are updated by appending the new
> information,
> the mdout and dist_vs_t files are not.
>
> Thus my question is if I am doing something wrong with the inputs or if I
> have to rename out and DUMPAVE files in every run.
>
Based on your observations, I think you need to give them separate names.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 12 2013 - 15:30:02 PDT
