Well, based on the one snapshot, I would argue that the simulation
certainly did not work correctly unless there is some sort of severe
visualisation artefact going on....
Not knowing anything about your system, or aMD, the first suggestion would
be to run a regular MD, check that your system behaves as you expect and
only retry an aMD run when you are sure regular MD works without issues.
In parallel, run a test of your aMD protocol on the simplemost system you
can come up with, something like ethanol in water or so, to check that that
behaves reasonably, too..
Kind Regards,
Thomas
On Mon, Jan 6, 2025 at 10:46 AM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> please response.
>
> On Sun, Jan 5, 2025 at 6:09 PM Dulal Mondal <
> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
> >
> > Dear Experts,
> > I am trying to run aMD simulation using amber24. I set the following
> > parameters in the mdin file
> > iamd=1,
> > ethreshp=-159511.27,
> > alphap=8490.88,
> >
> > aMD simulation runs properly. But when I visualize the trajectory I see
> > the following snapshotr of the protein.
> > Is this correct? If not, what can I do? How do I set the aMD parameter?
> > --
> > *With regards,*
> > *Dulal Mondal,*
> > *Research Scholar,*
> > *Department of Chemistry,*
> > *IIT Kharagpur, Kharagpur 721302.*
> >
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 06/OG07
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Mon Jan 06 2025 - 04:30:02 PST
