AMBER Archive (2009)

Subject: RE: [AMBER] PMEMD 10 overflow issues

From: Ross Walker (
Date: Fri Aug 21 2009 - 15:57:12 CDT

Hi Ben,

We need more information here to be able to help. What do you mean by
overflow? Simply the coordinates becoming too large? In GB this can occur
when you have initial translational motion and or use a thermostat. Setting
nscm = 1000 or so should alleviate this problem. In explicit solvent using
iwrap = 1 will fix it. If you are still seeing problems take a careful look
at your trajectory to make sure nothing strange is happening - such as it
blowing up.

All the best

> -----Original Message-----
> From: [] On
> Behalf Of ben rodriguez
> Sent: Friday, August 21, 2009 1:38 PM
> To:
> Subject: [AMBER] PMEMD 10 overflow issues
> Hello,
> Im trying to figure out why I am getting overflow issues using pmemd
> 10, for both explicit simulations and GB. AMBER 10 was compiled using
> intel 11.084 and openmpi. From what I have read the overflow issues can
> be avoided using iwrap, but this doesnt make sense to me under GB(
> althought there is a cavity bound water in the simulation).
> Does anyone has some insight here? Let me know if you need more info.
> Thanks,
> Ben Rodriguez
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