On Sat, Nov 16, 2013 at 11:26 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Hi all,
>
> I am running umbrella sampling calculations with generalized born implicit
> solvation using amber12 pmemd.MPI using the following input file. The
> simulation is running ok but it doesn't produce the distance output after
> each 100 steps as requested by the input file.
>
> Umbrella sampling of a distance
> &cntrl
> ntx=1, irest=0,igb=8,saltcon=0.2,gbsa=1,
> ntpr=100, ntwx=1000, ntwr=100,nsnb=1,
> nstlim=1000000, t=0.00, dt=0.00100,
> ntc = 2, ntf = 2,tol=0.000001,
> ntb = 0,
> ntt=3, temp0=300, tempi=300, ig=30759,gamma_ln=4, vlimit=20.0,
> cut = 40.0,
> nmropt=1,
> /
> &wt type='DUMPFREQ',istep1=100 /
> &wt type='END' /
> DISANG=dist.RST_998
> DUMPAVE=dist_vs_t_998
>
> The output is readily given in amber11 and amber10 but not in amber 12.
> Could anybody please suggest if I have overlooked something?
>
Try a short simulation (maybe 1000 steps or so) and see if the file gets
written correctly.
It may be a file buffering problem if you're not letting the simulation
finish.
>
> Thank you very much in advance
>
> Sajeewa Dewage
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Nov 16 2013 - 09:30:02 PST
