Re: [AMBER] Questions about softcore part

From: David A Case <>
Date: Thu, 10 Oct 2013 07:43:30 -0400

On Thu, Oct 10, 2013, yuandandan wrote:

> I used softcore potential for TI calculation.
> The error appeared as: vlimit exceeded for step…
> At first, I slowly heat the system up to 300K over 225 ps in a total of
> 15 stages,
> each stage with time step 0.5 fs, and 3000 steps.
> However, the MD production was failed once I set the timestep 1.0 fs.
> It seems that the system would fail with timestep 1.0 fs or longer.

Does this happen for all values of lambda? Do you have similar problems with
either V0 or V1 by itself? What happens if you don't use softcore? Is there
something unusual about this system? (That is, can you run most softcore
problems OK, but have problems only with this one system)?

There are many things that can cause instabilities. As you can see from the
questions above, you will need to spend some time trying to narrow down the

> However, the temperature following “Softcore part of the system:”
> oscilated violently.

This is normal, if (as is usual) only a few atoms are in the softcore region.


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Received on Thu Oct 10 2013 - 05:00:04 PDT
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