Fwd: About the robustness of ABF and FEB protein-ligand

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jun 28 2017 - 09:47:59 CDT

Clearly, however, running with ts=0.1fs with such demanding simulations for
a large system is no real solution. I was only happy that I could see the
procedures running.
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Jun 28, 2017 at 4:40 PM
Subject: About the robustness of ABF and FEB protein-ligand
To: NAMD <namd-l_at_ks.uiuc.edu>

I have been dwelling for some days on applying the ABF and FEP
protein-ligand tutorial, with a protein-organic-molecule in water boxes
rather than protein-peptide. Without any restraint to any atom (except
TIP3P water), ts=1.0fs. I posted the problems in detail.

No problem was encountered with the Unbound situations, while instability
of the system raised up systematically at the first step with the Bound
situation: atoms moving too fast, usually pertaining to the ligand, less
frequently to the receptor.

I changed the setting for "r" colvar from a directly measured value on VMD
to the value resulting from "cv printframe" (I was using the last frame of
a 58.2ns unbiased MD), something that is still not wholly clear to me. All
that at no avail.

The solution was got by further decreasing the integration, to ts=0.1fs,
whereby both ABF and FEP started running (I killed the simulations as I was
using a desktop, as at the moment I have no access to a cluster, while
these simulations (or FEP alone ?) do not run on my GPU workstation.

As the Bound system had never crashed during a 58.2ns unbiased MD at
ts=1.0fs on a pure-CPU cluster, my question is: are there in general more
stringent requirements of integration than with unbiased MD when running
without any restraint on any atom?
All such problems probably arose because I am not comfortable with
restraining H-atoms because it was never proven that they are equivalent to
not restraining. Is that care irrelevant to ABF and FEP because of larger
errors elsewhere?


francesco pietra

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