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?
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 - 03:30:02 PST
