[AMBER] Production run in NVT ensemble

From: Baptiste Legrand <bap.legrand.gmail.com>
Date: Fri, 14 Feb 2020 12:04:18 +0100

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:
https://ambermd.org/tutorials/advanced/tutorial21/section2.htm, 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?


Best regards

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 - 03:30:02 PST
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