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

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat Feb 24 2018 - 08:39:07 CST

Also, maybe I’m over-interpreting what you said Rabeta, but no one should rely on the NAMD tutorial as an exhaustive resource of what’s available, especially things that aren’t co-developed with NAMD. There are

all-atom: http://mackerell.umaryland.edu/charmm_ff.shtml#charmm <http://mackerell.umaryland.edu/charmm_ff.shtml#charmm>
and CG: http://cgmartini.nl/index.php/force-field-parameters/lipids2/351-lipid.html?dir=PS&lipid=POPS <http://cgmartini.nl/index.php/force-field-parameters/lipids2/351-lipid.html?dir=PS&lipid=POPS>

representations of POPS in their respective force fields.

Best,
JC

> On Feb 23, 2018, at 7:02 PM, Lutimba Stuart <lutimba.stuart_at_scilifelab.se> wrote:
>
> 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 <rabetayeasmin_at_gmail.com <mailto:rabetayeasmin_at_gmail.com>> wrote:
> 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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