AMBER Archive (2004)

Subject: Re: AMBER: Simulated annealing ...vlimit problem

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon May 17 2004 - 12:08:56 CDT

have you minimized the structure first? can you do "normal
MD" on this one too, not the protonated and hydrated one?
try to only change 1 thing at a time or else it is hard to track
down the problem.

your heating phase will be very fast and that can cause lots
of problems, especially with a poor initial structure.
why not add a step to heat to 600K over some period
of time?

carlos

> I have also done the normal MD on the same structure which went fine, but
> in this case I have protonated it and also hydrated it.
>

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