Thank you, that worked.
Abdullah
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, January 23, 2020 2:10 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Wanting to get synchronized trajectory files
try running without MPI.
On Wed, Jan 22, 2020 at 11:07 AM Abdullah Bin Faheem <
abdullahbinfaheem.hotmail.com> wrote:
> I am running the two CPU-based MD jobs using the same node of a linux
> based computer cluster (CentOS Linux release 7.7.1908) (CPU: Intel(R)
> Xeon(R) Gold 6152).
>
> Run Command:
> mpirun -np 4 sander.MPI -O -i mdsim.in -o mdsim.out -p an_mol.prmtop -c
> saved.rst -x mdsim.crd -e mdsim.en -r mdsim.rst
>
> Abdullah
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Thursday, January 23, 2020 12:43 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Wanting to get synchronized trajectory files
>
> this would only be possible on identical hardware - can you tell us more
> about how you are running the 2 jobs?
>
>
> On Wed, Jan 22, 2020 at 10:05 AM Abdullah Bin Faheem <
> abdullahbinfaheem.hotmail.com> wrote:
>
> > Thank you for your response. While using 100 steps produces the same
> > coordinates, noticeable deviations in the coordinate file begin to appear
> > after 3000 steps. Is it not possible to run longer trajectories? Say 50
> or
> > 100 ps without experiencing changes.
> >
> > Abdullah
> > ________________________________
> > From: David Case <david.case.rutgers.edu>
> > Sent: Wednesday, January 22, 2020 10:09 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Wanting to get synchronized trajectory files
> >
> > On Wed, Jan 22, 2020, Abdullah Bin Faheem wrote:
> > >
> > >Is it possible to get the same output trajectory file if I use the same
> > >topology and restart file?
> > >Meaning if I run two MD runs in parallel, can I get the same xyz (or
> > >atleast very close) coordinates being written in the output coordinate
> > >file if I use the same restart and topology file? This is the input file
> > >I used initially (I am currently using AMBER 12):
> >
> > What happenes when you tryrunning (say) two 100-step simulations?
> > Don't be afraid to experiment. Be sure to set ig (I'm not sure what the
> > default value for that was way back in 2010.)
> >
> > ....dac
> >
> >
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Received on Wed Jan 22 2020 - 11:00:01 PST
