AMBER Archive (2007)

Subject: Re: AMBER: multi chain simulations

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 04 2007 - 14:43:44 CDT

I suggest making changes to force.f.
right at the place that xconst() is called.
you can also add your energy into ene(20).
Make a copy of the xconst() routine and
rename the subroutine xsphere.
instead of comparing to xc like xconst does (the reference
coordinates), compare to the sphere boundary. using xconst will
help because the loops over atoms, etc are already set up.
the derivatives will look slightly different but you can work
out the correcct equations using the chain rule.

some pseudo code might be to
1) calculate the distance of the atom from the origin (sqrt(x^2+y^2+z^2)
2) if less than your sphere radius, don't add a force
3) if larger than the sphere radius, add a force to the atoms based on
something like a harmonic term k*(r-spheresize)^2
the derivatives will look similar to the ones in xconst since that also
uses a harmonic restraint. the difference is that zconst uses
the reference coordinates (a constant) and you will use a sphere
radius (also a constant).

if your programmer starts to work on it and has specific questions,
have them contact me directly.

On 10/4/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
>
> Dear Sir,
>
> I have colleagues who knows programming, so they can help me in this
> regard that is not a problem.
> But suggestion from your side needed in that respect.
>
> Regards
> priya
>
> *Carlos Simmerling <carlos.simmerling_at_gmail.com>* wrote:
>
> it's not really practical without knowing fortran or
> finding someone at your institution that can help you.
> I can tell you what to do in general terms but someone
> needs to write the code and test it. I suggest cheching
> for people locally and let us know if you can find a
> colleague that is experienced with programming and
> can help you.
>
> On 10/4/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
> >
> >
> > Dear Sir,
> >
> > I dont know much fortran.
> > BUt some suggestions for the changes would help me to do that.
> >
> > priya
> >
> > *Carlos Simmerling < carlos.simmerling_at_gmail.com>* wrote:
> >
> > you would need to write some code to do it.
> > do you know fortran?
> >
> > On 10/4/07, priya priya <priyaanand_27_at_yahoo.co.in > wrote:
> > >
> > > Dear All,
> > >
> > > I am trying to run MD using multi chain system in implicit solvent by
> > > setting up a box using setBox command in leap, but generalized born
> > > simulations can only be run for non-periodic systems, so the chains are
> > > diffusing away from each other during the simulation run.
> > > I want to create an imginary sphere around the molecule and if the
> > > distance of atom from the center of mass is longer than the length of the
> > > imaginary sphere, then, i want to apply additional force imposed on that
> > > atom (the direction is to the center of mass).
> > > What options can I use to keep the chains in a box (not flying far
> > > away from each other) whose sphere I am specifying.
> > > Any suggestions how to do it in amber9
> > >
> > >
> > > Regards
> > > priya
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