[gmx-users] Regarding REMD using gromacs4.5.5

[Amit Kumar]

Thank You Daniel Burns,
Actually, right now I am looking at the installation and trying to install
fresh as I found some error and created mess again while rectifying each
one. At the time of installation "mdrun_mpi -h" worked perfectly so I
thought installation is fine. But really thank you for your valuable inputs.

Amit Kumar

On Wed, Mar 4, 2020 at 7:39 PM Daniel Burns <dburns at iastate.edu> wrote:

> Hi Amit,
>
> I’m not the best resource for solutions but I’ve been having this issue
> with gromacs 2018.  It seems to be related to the process manager or our
> open mpi module we are using. The job would hang on some open mpi
> communication step.
>
> I found it would work if each replica was assigned its own entire node but
> that becomes prohibitively resource expensive with more than a few
> replicas.
>
> I was finally able to get it to work on our least used cluster where things
> must have been installed correctly.
>
> You might have your IT look at what’s happening with the process manager
> and open mpi or whatever dependencies you have loaded. You might try a
> small job where you can assign each replica to its own node and see if you
> get the full output. Our IT dept has been working for two weeks and still
> haven’t gotten it to work on the other clusters.
>
>
> Dan
>
>
> On Tuesday, March 3, 2020, Amit Kumar <amitkumar879792 at gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent
> > but I am unable to get any output file containing significant data
> (logfile
> > is obtained with only developers' details) or any error file.
> > I am unable to understand why this is happening and how can I tackle the
> > situation?
> > Kindly, help me out of this situation.
> >
> > ThankYou
> > Amit Kumar
> >
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