AMBER Archive (2009)

Subject: Re: [AMBER] Is it the way to do simulation in vacuum

From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Oct 30 2009 - 11:06:14 CDT

Nicholus,

ntb defaults to 1 (as seen in the manual). This is the setting for constant
volume periodic boundary conditions. You will have to set ntb=0 for
vacuum. I have seen cases where periodic boundary conditions are
incompatible with other input types, and it causes this behavior (pmemd
recognizes a mistake and exits with an error message, but sander does not,
and it appears to find itself in an infinite loop). Make sure you have all
of those parameters correct when you start your simulation (ntb may be the
only one you have to change, but don't quote me on that). You'll also want
to make sure that igb=0, but that is the default value.

Good luck!
Jason

On Fri, Oct 30, 2009 at 9:26 AM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> have you run the test cases?
>
>
> On Fri, Oct 30, 2009 at 7:11 AM, nicholus bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
>
> > On Fri, Oct 30, 2009 at 6:21 AM, Carlos Simmerling <
> > carlos.simmerling_at_gmail.com> wrote:
> >
> > > we need to see your sander input.
> > > also- what does your sander run script look like? if you do a "top" on
> > that
> > > machine, is sander still running?
> > >
> > > Dear community,
> > > > I am trying to simulate my protein in
> vacuum.
> > I
> > > am
> > > > preparing the topology and parameter files as follows
> > > >
> > > > $ tleap
> > > > > source leaprc.ff99SB
> > > > > mol=loadpdb pdb
> > > > > saveamberparm mol prmtop inpcrd
> > > > >quit
> > > >
> > > > Then I have run the minimization of 250 cycles. But this small
> > > minimization
> > > > is not coming out. And investigating the output file by "tail -f"
> > command
> > > > only shows the following
> > > > --------------------------------------------
> > > > AMBER 9 SANDER 2006
> > > > --------------------------------------------
> > > >
> > > > I am unable to find the defect in the procedure. Please help.
> > > >
> > > > --
> > > > Nicholus Bhattacharjee
> > > > PhD Scholar
> > > > Department of Chemistry
> > > > University of Delhi
> > > > Delhi-110007 (INDIA)
> > > > Phone: 9873098743(M)
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER_at_ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > The input file is
> >
> > Minimization of the entire molecular system
> > &cntrl
> > imin=1, maxcyc=250,
> > ntpr=5,
> > &end
> >
> >
> > I am running sander as
> >
> > $ sander -O -i inputfile -p prmtop -c inpcrd -o outputfile -r restrtfile
> >
> > Yes sander is running when when I top. By the way do I have to make ntb=0
> > in
> > the input file?
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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