Hi Dan,
Thanks for your reply,
Pls have a look at the input and the command line i used for the production
run.
heat
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0, ig=-1,
/
srun --gres=gpu:2 pmemd.cuda.MPI -O -i ./input-files/6-prod.in -o prod2.out
-p mcl1-cm5-solvated.prmtop -c equil1.rst -r prod2.rst -x prod2.mdcrd
Thanks,
M.P.
Message: 21
> Date: Thu, 20 Jul 2017 09:27:56 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Log file for Reweighting
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qObU1P3wCQKK2YahRmLhgMeo3gdMXRW81_zY0yPBw5qgwQ.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> What was the input you gave to sander (or pmemd)? What was the command
> line you used to execute the program?
>
> -Dan
>
> On Wed, Jul 19, 2017 at 3:48 PM, Parthiban Marimuthu <mparthib.gmail.com>
> wrote:
> > Dear Amber users,
> >
> > I am resubmitting the my query again as it was not discussed.
> >
> > I am trying to plot phi_psi dihedral angles using the python reweighting
> > script from the following tutorial.
> > http://ambermd.org/tutorials/advanced/tutorial22/section3.htm
> >
> > The reweighting tutorial explains that creating a weights.dat file from
> > amd.log file.
> >
> > I followed both cMD & aMD using Amber16 individually from which I see
> there
> > is NO log file created for some reason.
> > All i have is .out, .rst and .nc files only.
> > As the tutorial explains, .log file is the starting file to create
> > weights.dat file, i cannot proceed further.
> >
> > I believe i am missing or misinterpreting with other files.
> >
> > Kindly suggest.
> > M.P.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
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Received on Thu Jul 20 2017 - 13:30:03 PDT
