AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Oct 30 2009 - 14:15:01 CDT

Remember to also set cut=9999.0 so you do not get a cutoff which you do not
want if you really want to do a vacuum simulation.

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Carlos Simmerling
> Sent: Friday, October 30, 2009 9:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Is it the way to do simulation in vacuum
>
> a good approach is to start with a test case or tutorial that works and
> does
> something similar to what you want, and modify it from there. if
> something
> stops working you know what you changed.
>
>
> On Fri, Oct 30, 2009 at 12:06 PM, Jason Swails
> <jason.swails_at_gmail.com>wrote:
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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