Re: [AMBER] AMBER Digest, Vol 1311, Issue 1

From: Jason Swails <>
Date: Sat, 15 Aug 2015 09:21:17 -0400

On Sat, Aug 15, 2015 at 4:58 AM, Robin Jain <>

> Dear all,
> I have used following MEOH parameters, Will you please check this and find
> the problem.

​There is nothing that seems very wrong with your frcmod or prepin files.
As a result, it is impossible to find the problem without running the
simulations exactly as you did, and I doubt anybody on the list has either
the time or computational resources to spare for that.

Also i want to state that first i minimize my system , the heat and then
> equilibration and production run.will u required input file also to know
> about my problem.

​The only thing I can think of given the amount of information you've
provided is to make sure that at *some* point you run constant pressure
dynamics to make sure that the density has equilibrated. Another good
thing to check is the equilibrated density -- that should be close to the
experimental value of the density, or the nonbonded parameters (i.e.,
charges and/or van der Waals) likely need to be improved.​
  There has been a lot of work regarding using the densities of neat
liquids and binary mixtures to improve nonbonded parameters -- survey the
literature to see what these groups have done.

If the density is wrong, so too will be the RDF.

> Please solve my problem. Thanking You.
> ​​

​This is a typical problem associated with a research project, not a
technical challenge about running Amber. You will need to do a lot of this
work on your own, and consult the list with specific questions.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Aug 15 2015 - 06:30:03 PDT
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