[gmx-users] Regarding REMD using gromacs4.5.5

[Mohammad Madani]

Hi Amit
Could you please send me your mdp file for implicit solvent remd?

Many thanks

On Thu, Mar 5, 2020 at 5:07 AM Amit Kumar <amitkumar879792 at gmail.com> wrote:

> *Message sent from a system outside of UConn.*
>
>
> 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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