Sorry to have not replied to this, but I've been really busy.
In Sander for AMBER6, this is possible using a new namelist
flag VRAND. However, you need to change the MACHINE file
to enable the option, it needs -DV_RAND in the MACHINEFLAGS line.
then use vrand=# in your sander input, it will reassign velocities each vrand steps.
Carlos
Robert Matthew Fesinmeyer wrote:
> I noticed this question went unanswered. I believe that the way you do
> this is to use the NRUN variable in combination with the NSTLIM and DT
> variables. Thus instead of running one 1ns run (NRUN=1, and
> DT*NSTLIM=1ns), you'd set NRUN=2 and DT*NSTLIM=500ps. I believe this
> would allow the run to go for 1ns, but would reassign the velocities after
> 500ps.
>
> I hope that someone will confirm or deny this statement.
>
> As a sidenote, is there a consensus opinion to the reassignment of
> velocities for a problematic system? Is once per 200ps generally thought
> of as valid, but not, say, once per 10ps?
>
> Thanks,
> Matt
>
> _________________________
> R. M. Fesinmeyer
> rmf_at_u.washington.edu
> Department of Chemistry
> University of Washington
>
> On Fri, 11 Aug 2000, Raik Gruenberg wrote:
>
> > Hi,
> >
> > is it possible to prompt sander to reassign velocities from a Maxwell
> > distribution such and such often in the course of a MD run?
> > I faced some difficulties to equilibrate my protein and the only
> > work-around I have come up with so far is to restart the simulation
> > several times.
> >
> > Thanks for any advise
> > and have a nice weekend!
> >
> > Ciao
> > Raik
> > ____________________________
> > Raik Gruenberg
> > gruenber_at_embl-heidelberg.de
> > www.raiks.de/contact.html
> >
> >
--
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336 NOTE NEW AREA CODE
Department of Chemistry Fax: (631) 632-7960
SUNY at Stony Brook Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-3400 E-mail: carlos.simmerling_at_sunysb.edu
===================================================================
Received on Wed Aug 23 2000 - 09:41:17 PDT
