AMBER Archive (2005)

Subject: Re: AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble.

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 22 2005 - 13:56:36 CST

On Thu, Dec 22, 2005, Sergey Krishtal wrote:
>
> I solvated some peptide in water by AMBER 8 solvatebox command, performed
> minimixation and equilibration (1 ns) in the NVT-ensemble at 298 K. Then, I
> performed eqilibration in the NPT ensemble at 1 atm for rather long time (1
> ns). Now I want to use the box obtained in NVT simulations at 305 K.
> However, when I run such simulation Amber crashes without giving any error
> message except for the batch system message like that below:

There is no reason why using NVT per se should be related to a crash. Of
course, you should try your job in serial mode to see if you can find the
error there. Try to just run it interactively (avoiding a batch system),
since sometimes error messages can get swallowed by a batch system.

...good luck....dac

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