Hi,
You have no AMD options set (e.g. 'iamd' namelist variable etc) which
is why you get no AMD output.
-Dan
On Thu, Jul 20, 2017 at 4:23 PM, Parthiban Marimuthu <mparthib.gmail.com> wrote:
> 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
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 20 2017 - 14:30:03 PDT
