AMBER Archive (2004)

Subject: Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander

From: Robyn Ayscue (kajsicat_at_yahoo.com)
Date: Thu Jun 17 2004 - 10:35:34 CDT

Thanks to everyone who helped me on this. I removed
the &rst tag from my .in file and, while there were a
few vlimit errors in the very beginning of the run, it
seemed to overcome them and finished out just fine.
Again, many thanks.

Yours,
Robyn Ayscue

--- Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> I think that is because sander was using a negative
> force constant
> for the restraints, because of the problem I posted
> earlier.
> carlos
> ----- Original Message -----
> From: "Andreas Svrcek-Seiler"
> <svrci_at_tbi.univie.ac.at>
> To: <amber_at_scripps.edu>
> Sent: Wednesday, June 16, 2004 10:58 AM
> Subject: Re: AMBER: Trouble running molecular
> dynamics with an increase in
> temp in Sander
>
>
> > Hi,
> > Your RESTRAINT enery seems to drop to -infinity,
> being converted into
> > kinetic energy (->vlimit). I'm not familiar with
> the Amber-restraint
> > options, but I think you should have a close look
> at them.
> >
> > I hope that helps,
> > regards
> > Andreas
> >
> > --
> >
> > )))))
> > (((((
> > ( O O )
> >
>
-------oOOO--(_)--OOOo----------------------------------------------------
> -
> > o Wolfgang Andreas
> Svrcek-Seiler
> > o (godzilla)
> > svrci_at_tbi.univie.ac.at
> > .oooO Tel.:01-4277-52733
> > ( ) Oooo.
> > -------\
> ---(
>
)--------------------------------------------------------
> > \_) ) /
> > (_/
> >
> >
> >
>
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