AMBER Archive (2009)

Subject: RE: [AMBER] PMEMD 10 overflow issues

From: ben rodriguez (bramber_at_live.com)
Date: Fri Aug 21 2009 - 16:17:36 CDT

I should have said that I am getting corrupted restart files for the explicit solvent simulations, due to what I think is overflow (****** where values should be). Nothing unusual is happening to my structure, its definitely not blowing up. What I also dont understand is that the restart file should be the last set of coordinates from my trajectory, but my trajectory file does not appear to be corrupted.

Ben

> From: ross_at_rosswalker.co.uk
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] PMEMD 10 overflow issues
> Date: Fri, 21 Aug 2009 13:57:12 -0700
>
> 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
> Ross
>
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > Behalf Of ben rodriguez
> > Sent: Friday, August 21, 2009 1:38 PM
> > To: amber_at_ambermd.org
> > 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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