Re: [AMBER] Is this output OK from the hybrid remd?

From: Jason Swails <>
Date: Fri, 17 Dec 2010 22:37:41 -0500


I think your problem lies in the use of coordinate restraints with hybrid
REMD. One of the steps that hybrid REMD has to do is reimage all of the
water molecules and place it at the location of its closest periodic image
since GB methods are inherently non-periodic and know nothing about
alternate images.

One of the things done in "subroutine stripwat" in remd.f is the centering
of the entire system with respect to its center of mass. The reason I think
you are having issues is that the coordinates are adjusted by the center of
mass position, but the reference coordinates are never adjusted.

I'm not positive this will work, but I included a patch which will adjust
the reference coordinates in exactly the same way as the normal
coordinates. Apply it to the latest, fully patched amber11 from AMBERHOME.

patch -p0 -N < hybrid_remd.patch

Then recompile. Also please report back whether it worked or not. One
other thing to try that probably should've been mentioned before is testing
to see that it worked if you don't include restraints, just to make sure
that it is in fact the restraints that are causing the issue.

Hope this helps,

On Fri, Dec 17, 2010 at 11:43 AM, Bongkeun Kim <> wrote:

> Quoting case <>:
> > On Fri, Dec 17, 2010, Bongkeun Kim wrote:
> >>
> >> I just run the hybrid remd and checked the output file.
> >> It said ********** on EPot. Does it mean only the number is too big to
> >> print or is there any problem on this run?
> >
> > There seems to be a problem with the restraint energy:
> >
> >> EELEC = -6589.2279 EGB = -3004.6220 RESTRAINT
> >> =57092146.9150
> >
> > You can't run replica exchange simulations with ntr>0 (unless, I guess,
> that
> > all replicas have the same reference structure. Also, be sure that you
> can
> > sucessfully run non-exchange simulations at each temperature of interest.
> >
> I already tried to run it with full explicit water and it gave me no
> problem. But this run demands too many resources.
> With hybridgb, EPtot = 58053860.3203 and
> Without hybbridgb, EPtot = 546283.2545.
> Also, RESTRAINT = 57444151.6840 with hybridgb and
> RESTRAINT = 177.4334 without hybridgb.
> It seems like the hybridgb method overestimates restraint energy of my
> graphite surface too much. I checked the structure of whole system.
> The peptide lies on the graphite surface now. I think explicitly
> considered water molecules by numwatkeep=500 are on the other side of
> graphite surface, that is across the surface. Do you think this makes
> problems?
> Thank you.
> Bongkeun Kim
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student

AMBER mailing list

Received on Fri Dec 17 2010 - 20:00:02 PST
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