Re: Coarse-grained umbrella sampling for POPS-protein system

From: Lutimba Stuart (
Date: Fri Feb 23 2018 - 18:02:53 CST

Hello Rabeta, please provide the configulation file the you used, such that
this can be followed its usually a combination factors resulting from the
force constant used to the atom selection.

On Sat, Feb 24, 2018 at 12:53 AM, Rabeta Yeasmin <>

> Dear NAMD users,
> I am running coarse-grain umbrella sampling simulation for a POPS-protein
> dimer system. I have used residue based coarse-graining method to convert
> all-atom system to coarse-grained system. As NAMD tutorial did not provide
> mapping and topology files for POPS lipid; according to suggestions from
> this group, I had modified those two files of POPE at the head position
> for POPS. But I am getting undesirable potential mean force result after
> running around 50ns. I am not sure
> There was I would be grateful if anyone can suggest me about this.
> Thanks.
> Rabeta Yeasmin

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