Hi Jason,
Yes, you are correct. It waits until the end to give the distance output.
Thank you very much.
Sajeewa
On Sat, Nov 16, 2013 at 12:19 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Sat Nov 16 2013 - 10:30:02 PST
