Re: [AMBER] Production run in NVT ensemble

From: Carlos Simmerling <>
Date: Fri, 14 Feb 2020 06:34:51 -0500

There should be no need for you to add such a line to your rst7, it will be
generated automatically if you set the ntb variable. Perhaps your solvent
looks dispersed because you did not use iwrap=1? Try using cpptraj and
autoimage on your trajectory.
If this is not the problem then please send your entire input files
starting from the first run.

On Fri, Feb 14, 2020, 6:04 AM Baptiste Legrand <>

> Dear all,
> I compared production run in NPT and NVT ensemble for a protein
> complexe. I saved about 30% of time at constant volume. Nevertheless, as
> I did not specified the volume of the solvent box as indicated in the
> following tutorial:
>, and the
> water molecules are dispersed in a large volume.
> Thus, I add the following line during the equilibration as indicated,
> the box is not exactly cubic but rectangular:
> &ewald nfft1=80, nfft2=60, nfft3=60, order=4 /
> then I calculated the average box edge from the average volume =>
> 61.3534403, then I converted the final ncrst to rst7 to modify the
> latest restart file adding the box lengths as indicated.
> As the box is not really cubic, is it a strong approximation to add
> 61.3534403 61.3534403 61.3534403 90.0 90.0 90.0 in the rst7 file to
> start the production run at NVT and where should I add this line?
> Thanks,
> Best regards
> Baptiste
> IBMM, University of Montpellier
> ps: thanks again Elvis for your answer last week, I forgot to
> re-activate the mail delivery for the amber list.
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Received on Fri Feb 14 2020 - 04:00:02 PST
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