From: Radak, Brian K (bradak_at_anl.gov)
Date: Tue Aug 09 2016 - 10:22:59 CDT
Can you elaborate on "does not converge well"? Is the convergence just slower? If so, how are you judging this? Is the system unstable? Are your force field settings standard or is anything unusual going on (besides the fixed particle, which is likely unnecessary)?
I exclusively use NVT for free energy computations, but don't do annihilation that often.
In general I would expect the NVT protocols to be simpler and more stable than the NpT protocols, but that's just a gut feeling. Also, there is some fudginess about how the kinetic virial is computed when using the alchemy modules (and probably Cartesian constraints also), so I try to avoid this when possible. Your idea to equilibrate the density first and then turn on alchemy is, in my opinion, the right one.
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From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of B.W.J. Irwin [bwji2_at_cam.ac.uk]
Sent: Tuesday, August 09, 2016 5:22 AM
Subject: namd-l: Is it possible to perform NVT FEP on a fluid system?
I am trying to perform an FEP calculation on a box of neon with a fixed
central neon atom which annihilates.
It works well in the NPT ensemble and convergence is reached, but when I
remove the pressure regulation and set the volume, the corresponding NVT
calculation does not converge well. I would rather keep the volume of
the box constant.
I read in "Re: Query Regarding FEP tutorial: NPT or NVT?", "use NPT for
solvated system and just constant temperature for in vacou simulations".
Is it possible to perform NVT FEP on a fluid system and reach
convergence with NAMD?
Thanks in advance,
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