AMBER Archive (2005)

Subject: Re: AMBER: Cluster - input files

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 28 2005 - 15:28:14 CST

On Mon, Nov 28, 2005, Ananda Rama Krishnan Selvaraj wrote:

> I am sorry for the confusion. yes, i tried to
> make a MD simulation using Periodic Boundary Condition. In AMBER5 as
> well as AMBER7 in both case i have used the same pdb file to make prmcrd
> files. But the outfile from the (AMBER7) LEaP (prmcrd)has more volume
> than in AMBER5.

My best guess is that this is expected. Amber 7 tends to make a system
with relatively low initial density, that will increase as the equilibration
takes place.

>
> I don't know exactly which could be the reason for the error. so that i
> have mentioned the LEaP commands,

Since you only gave the LEaP commands you used for the non-periodic
simulation, it's hard to know whether or not you did anything wrong (or less
than optimal) when you actually used LEaP to prepare the periodic simulation.
In particular, you might play around with the closeness parameter in the
solvateBox or solvateOct commands: try something like 0.75. (Of course, you
may have already done this....)

...dac

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