[gmx-users] How to build and simulate POPE/POPG bilayer with gromos54a7 force field

[Justin Lemkul]

On 11/4/19 9:05 AM, daniel depope wrote:
> I want to simulate POPE/POPG bilayer with gromos54a7 ff (expanded with
> lipids parts, as explained in Lemkul's kalp tutorial).
>
> 1. I tried CHARMM-gui website - I got bilayer in step 5, but can't finalize
> because there are no gromos ff option. So I looked for pope and popg
> gromos54a7 topology, but with no succes so I stacked. Any suggestions how
> to proceed?

CHARMM-GUI is intended for use with the CHARMM force field, so this is 
to be expected.

> 2.  Another option was to build that bilayer with packmol, but I can't find
> a way to do so (I know how to build homogenuos bilayer).
>
> 3. POPE molecule from CHARMM-gui website have 125 atoms. I have some old
> POPE molecule with only 52 atoms. Last one has only two hydrogen atoms. Can
> anyone explain why is that a case.

CHARMM is an all-atom force field. GROMOS is united-atom.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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