Re: [AMBER] NaN error in .rst files

From: Ross Walker <>
Date: Wed, 26 Jan 2011 19:05:00 -0800

> a minute). Then it stabilizes itself at this temperature. The actual
> simulation consists of many 500 pico second runs. I decided to use
> this time scale right after i had this NaN errors in the first time.
> My reasoning based on the observation of first set of NaN s in a
> longer run. Back in that time fine part of the .rst file was close to
> 800 pico seconds. Then this leads me to divide it into 500 pico second
> steps. Again for those runs, i am using a cutoff distance 10 A.
> iwrap=1 flag/options is included. But, I am not utilizing ig=-1
> flag/option. Basically my input file is exactly same with the input
> file
> in advanced web tutorial for explicit solvent case except this iwrap

"but I am not utilizing ig=-1"

Don't do this..., unless you are setting the ig value manually to a
different value for each restart. If you are using ntt=3 this can be


All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Wed Jan 26 2011 - 19:30:04 PST
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