AMBER Archive (2006)

Subject: Re: AMBER: restraints and constant pressure

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Sat Sep 16 2006 - 23:38:06 CDT

> Just to make sure I am understanding correctly: The scaling process
> changes the relative positions of separate protein chains, but it does
> not change the relative positions of the atoms within a given protein
> chain. Is that correct?

Yes, if you are using recent versions of AMBER, or if NPSCAL=1

> If I need to edit the prmtop file to represent everything as a single
> chain, how would I go about doing that? If I have already run several
> simulations using the old prmtop file, is it okay to edit it now,
> mid-way through the sequence of simulations?

As is wise at any step of MD simulation, it is useful to visualize what is
going on and try to determine if it makes sense.

The constant pressure scaling with restraint artifacts are fairly obvious,
so if there is an artifact so far, you should be able to see it.

Changing now, is OK if you haven't seen artifact. The archives should
have detailed info on how to do the merge and if you need more guidance,
e-mail me offline.

--tom

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