AMBER Archive (2007)

Subject: Re: AMBER: TIP4P MD simulations

From: Melinda Layten (mlayten_at_gmail.com)
Date: Mon Jul 09 2007 - 13:05:39 CDT

The changing cutoff shouldn't be the problem.

Did you run a minimization after creating your file?
Is there a very high initial energy caused by an overlap?

Spending some time on a careful minimization and equilibration gives you
much better results overall.

Good luck,

Melinda

On 7/9/07, Hashem Taha <hashemt_at_gmail.com> wrote:
>
> Hi There,
>
> i am trying to do MD simulation on a monosaccharide in TIP4P water. I
> have tried the simulation with TIP3P and it worked perfectly. Using
> the same input files but with TIP4P did not work because of the
> nonbonded cutoff of 8 angstroms. So i changed the cut from 8 to 7.5,
> and the simulation started. however, after about 14 ns of the
> simulation, it stopped and i received an error at the end of the
> output file:
>
> "cutoff list exceeds largest sphere in unit cell!"
> "big problems with imaging!"
>
> has anyone encountered this problem before.
>
> If you have any suggestions as to what i might be doing wrong.
>
> Also, throughout the output file, there are messages at some time steps
> that say
>
> "vlimit exceeded for step *****"
>
> please help
>
> HT
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