Re: AMBER: TIP4P MD simulations

From: Robert Duke <>
Date: Mon, 9 Jul 2007 15:35:04 -0400

Is this perhaps a really small unit cell at the start, somewhere between
15-20 angstrom on a side? Are you running an NPT ensemble, where if you
start with a density < 1.00, the box size will decrease? Are you using the
default skinnb value? As Dave mentioned, you may have other problems also,
perhaps relating to not setting things up properly. What we have here is
another of the many cases of "not enough info to really be able to help the
Regards - Bob Duke

----- Original Message -----
From: "Hashem Taha" <>
To: <>
Sent: Monday, July 09, 2007 1:53 PM
Subject: AMBER: TIP4P MD simulations

> 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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Received on Wed Jul 11 2007 - 06:07:33 PDT
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