VMD-L Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon May 20 2019 - 11:07:44 CDT

Hello Alex,

As part of my Master's thesis, which involved several Martini CG
simulations with NAMD, I had converted the original Martini cholesterol
model from the GROMACS itp format to the NAMD rtf/prm format.  I had
also made a cgc file for the conversion from CHARMM36 to Martini with
VMD's CG builder.  The files are still available here:

http://hector.biol.uoa.gr/~fbaltoumas/CoarseGrained/MARTINI/NAMD/cholesterol/

I hope they help you.  Make sure to read the "readme.txt" file included
in the link.  Briefly, consider the following points:

1.  The files follow the naming scheme of cholesterol in CHARMM36
(CHL1).  Make sure your all-atom cholesterol is modeled using CHARMM36.

2. The Martini files included are for cholesterol only.  You will need
to get the rest of Martini yourself from the TCBG link
(http://www.ks.uiuc.edu/Training/Tutorials/martini/).

3.  Due to the lack of constraints support in NAMD, all bond constraints
of the original topology are implemented as normal bonds, but with
higher force constant values (the same trick was done by the NAMD people
for the constraints in Phe, Tyr etc in the Martini protein force field).

4.  Simulation systems (a popc/cholesterol bilayer is given as an
example) are most stable with a 10 fs timestep value.  A 20 fs value may
also be used, but it may lead to crashes (due to point No. 3).  You can
forget about using 30 fs, it will crash with a 100% certainty within the
first few nanoseconds.  I would advise you use the 10 fs value,
especially if you define extrabonds parameters for your protein, or
apply an elastic network.

5.  This is the original cholesterol model (the one in the Martini paper
from 2007), NOT the updated one from 2016 (which uses virtual sites, a
feature not available in NAMD.

I hope this helps you.

Fotis

On 20-May-19 18:45, Alexander Adams wrote:
> Dear VMD users,
>
> I am looking to perform Martini simulations of a protein in membrane.
> VMD's CG builder has files for my protein and lipid components
> excluding the cholesterol molecules. I have an itp file from the
> Martini website with a CG cholesterol model to convert based on other
> cgc files, but wanted to check if anyone has already converted this to
> a cgc or has scripts to ease the process.
>
> Thanks in advance,
> Alex Adams
> --
> University of Michigan, Ann Arbor
> Ph.D. Candidate - Mayes, Glotzer Labs
> College of Engineering - Chemical Engineering 

-- 
Fotis A. Baltoumas, Bsc, Msc
Phd Candidate, Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology
National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
    --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
Tel.: +30 2107274876
Mob.: +30 6979258570
---
This email has been checked for viruses by Avast antivirus software.
https://www.avast.com/antivirus