Re: AMBER: multi chain simulations

From: priya priya <>
Date: Thu, 4 Oct 2007 13:44:56 +0100 (BST)

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.


Carlos Simmerling <> 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 <> wrote:
Dear Sir,

I dont know much fortran.
BUt some suggestions for the changes would help me to do that.


Carlos Simmerling <> wrote: you would need to write some code to do it.
do you know fortran?

 On 10/4/07, priya priya < > 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

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Received on Sun Oct 07 2007 - 06:07:25 PDT
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