[gmx-users] mdrun cpt

Mon Oct 28 21:07:36 CET 2013

You're welcome

On 28 Oct 2013, at 20:03, Pavan Ghatty <pavan.gromacs at gmail.com> wrote:

> Aah yes of course. Thanks James.
> 
> 
> 
> On Mon, Oct 28, 2013 at 3:16 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
> 
>> No this isn't a problem. You can use job names under the -hold_jid flag.
>> As long as you change the job name in the submit script between
>> submissions this isn't a problem. You could have a submit script for job 4
>> with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and
>> -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as
>> you have made this change which will be within seconds of submitting job
>> 4.
>> 
>>> Mark,
>>> 
>>> The problem with one .tpr file set for 100ns is that when job number
>> (say)
>>> 4 hits the wall limit, it crashes and never gets a chance to submit the
>>> next job. So it's not really automated.
>>> 
>>> Now I could initiate job 5 before /mdrun/ in job 4's script and hold job
>> 5
>>> till job 4 ends. But the PBS queuing system is sometime weird and takes a
>>> bit of time to recognize a job and give back its jobID. So I could submit
>>> job 5 but be unable to change its status to /hold/ because PBS does not
>>> return its ID. Another problem is that if resources are available, job 5
>>> could start before I ever get a chance to /hold/ it.
>>> 
>>> 
>>> 
>>> 
>>> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham
>>> <mark.j.abraham at gmail.com>wrote:
>>> 
>>>> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty <pavan.gromacs at gmail.com
>>>>> wrote:
>>>> 
>>>>> I have need to collect 100ns but I can collect only ~1ns (1000steps)
>>>> per
>>>>> run. Since I dont have .trr files, I rely on .cpt files for restarts.
>>>> For
>>>>> example,
>>>>> 
>>>>> grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
>>>>> 
>>>>> This runs into a problem when the run gets killed due to walltime
>>>> limits. I
>>>>> now have a .xtc file which has run (say) 700 steps and a .cpt file
>>>> which
>>>>> was last written at 600th step.
>>>> 
>>>> You seem to have no need to use grompp, because you don't need to use a
>>>> workflow that generates multiple .tpr files. Do the equivalent of what
>>>> the
>>>> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
>>>> .tpr
>>>> for the whole 100ns run, and then keep doing
>>>> 
>>>> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
>>>> 
>>>> with or without -append, perhaps with -maxh, keeping whatever manual
>>>> backups you feel necessary. Then perhaps concatenate your final
>>>> trajectory
>>>> files, according to your earlier choices.
>>>> 
>>>> - To set up the next run I use the .cpt file from 600th step.
>>>>> - Now during analysis if I want to center the protein and such,
>>>> /trjconv/
>>>>> needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
>>>> know
>>>>> to stop at 600th step?
>>>> 
>>>> 
>>>> trjconv just operates on the contents of the trajectory file, as
>>>> modified
>>>> by things like -b -e and -dt. The .tpr just gives it context, such as
>>>> atom
>>>> names. You could give it a .tpr from any point during the run.
>>>> 
>>>> Mark
>>>> 
>>>> If this has to be put in manually, it becomes
>>>>> cumbersome.
>>>>> 
>>>>> Thoughts?
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 10/27/13 9:37 AM, Pavan Ghatty wrote:
>>>>>> 
>>>>>>> Hello All,
>>>>>>> 
>>>>>>> Is there a way to make mdrun put out .cpt file with the same
>>>> frequency
>>>>> as
>>>>>>> a
>>>>>>> .xtc or .trr file. From here
>>>>>>> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
>>>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see
>> that
>>>> we
>>>>>>> can choose how often (time in mins) the .cpt file is written. But
>>>>> clearly
>>>>>>> if the frequency of output of .cpt (frequency in mins) and .xtc
>>>>> (frequency
>>>>>>> in simulation steps) do not match, it can create problems during
>>>>> analysis;
>>>>>>> especially in the event of frequent crashes. Also, I am not storing
>>>> .trr
>>>>>>> file since I dont need that precision.
>>>>>>> I am using Gromacs 4.6.1.
>>>>>> What problems are you experiencing?  There is no need for .cpt
>>>> frequency
>>>>>> to be the same as .xtc frequency, because any duplicate frames
>>>> should
>>>> be
>>>>>> handled elegantly when appending.
>>>>>> 
>>>>>> -Justin
>>>>>> 
>>>>>> --
>>>>>> ==============================**====================
>>>>>> 
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Postdoctoral Fellow
>>>>>> 
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 601
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>> 
>>>>>> jalemkul at outerbanks.umaryland.**edu
>>>> <jalemkul at outerbanks.umaryland.edu
>>>>> 
>>>>> | (410)
>>>>>> 706-7441
>>>>>> 
>>>>>> ==============================**====================
>>>>>> --
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>> * Please search the archive at http://www.gromacs.org/**
>>>>>> Support/Mailing_Lists/Search<
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>>>>> http://www.gromacs.org/Support/Mailing_Lists>
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> 
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists