Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system

From: David Case <>
Date: Thu, 15 Nov 2018 21:30:24 +0000

On Thu, Nov 15, 2018, Chetna Tyagi wrote:
>Upon carrying out accelerated MD on a peptide solvated in water and
>chloroform solvents in *Amber14 pmemd.CUDA.MPI*, I realized that when boost
>to the potential is applied to the Chloroform system, the various values in
>the output result in asterisks....
>For e.g. NSTEP = 1000 TIME(PS) = 2506002.013 TEMP(K) =*********
>Based on previous answers, the problem can be traced to high wrapping
>values which was,
>*wrapping first mol.: 136974.67863 1318602.52880 -1118357.40723*
>I used *iwrap =1* option in both cases.

The bad wrapping numbers look more like a downstream problem, caused by
some earlier problem; but I could be wrong. What happens if you run a
short simulation (since the problem appears already at step 1000),
setting iwrap=0? You might also print much more often (i.e. set ntpr=1)
to get more clues about what might be going wrong.

....good luck...dac

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Received on Thu Nov 15 2018 - 14:00:01 PST
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