[gmx-users] Extending simulation problem.

[Mark Abraham]

On Thu, Aug 21, 2014 at 6:28 PM, Dawid das <addiw7 at googlemail.com> wrote:

> Well in my *log file nothing about state or *cpi files is mentioned.
>

Sounds like perhaps your combination of circumstances (-append, no old
output files provided for appending, maybe not even a checkpoint file
provided) is leading to mdrun silently doing the only thing it can do,
which is start again from either the -s or -cpi state. Your description of "I
tried both state.cpt and prev_state.cpt and the beginning of new simulation
looks exactly the same" doesn't help fully - same as what? The start of the
first simulation, or the end of the first simulation?

There are some technical reasons why less output might be written when
doing mdrun -cpi -append, but your description does not make clear whether
they apply.

Acutally I have a question regarding state.cpi files. Does it contain names
> of *gro, *trr, etc. files if they are not standard?
>

Yes, even if not standard. You can see this with gmx dump -cp state.cpi


> The thing is, that output files from my first 5ns simulation are not
> standard. Now, I perform these calculations not in my working directory but
> on separate scratch.
> In this case, should the output files from previous simulation be present
> in the scratch?
>

You need to provide the files, however they are named, if you want to do
appending.


> And when I run another 5 ns should I run mdrun with those -c -o and -e
> options?


Yes, or use the -deffnm option to save yourself typing (and errors).


> If yes, should the names of files be the same as in the previous
> simulation?
>

Yes. Or use mdrun -noappend and do your concatenation later, old-school
style.

Mark


>
> 2014-08-20 18:18 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 8/20/14, 6:33 AM, Dawid das wrote:
> >
> >> Dear Gromacs experts,
> >>
> >> I googled for answer and I found these:
> >> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> >> http://www.researchgate.net/post/How_to_extend_the_
> >> protein_simulation_in_Gromacs_from_1000_ps_to_10000_ps
> >>
> >> but still I am confused about what happens in my simulation. I did 5 ns
> >> simulation and I would like to add extra 5 ns on top of that so that new
> >> results (energies, temperature, trajectory, etc.) will be appended to
> >> already existing files after first 5 ns simulation. Now I used this
> >> command
> >> to run MD simulation for the first time:
> >>
> >> \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro
> -e
> >> mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1
> >>
> >> After this in the same directory I run:
> >>
> >> tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr
> >> \$MDRUN -s npt-md-ext.tpr -cpi state.cpt
> >>
> >> I tried both state.cpt and prev_state.cpt and the beginning of new
> >> simulation looks exactly the same
> >>
> >> that means temperature, energies, etc. are the same as if I started
> >> from 0ns step, not from 5ns step of
> >>
> >> previous simulation. What can cause that? Is it because of used files
> >> names or I did something else wrong?
> >>
> >>
> > What does the .log file say?  It should clearly indicate if the restart
> > was done by reading in the checkpoint file.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA 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 | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>