[gmx-users] charmm c36 lipids

Pär Bjelkmar bjelkmar at cbr.su.se
Mon Oct 4 10:56:14 CEST 2010

> Date: Fri, 1 Oct 2010 16:27:29 +0100
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> Subject: Re: [gmx-users] charmm c36 lipids
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CA5FDE1.8050309 at soton.ac.uk>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

> For a POPC bilayer then both your and my files produce the same tpr's 
> (checked both with gmxcheck and gmxdump). This is pleasing as I not only 
> scripted the conversions but did some parts by hand! I shall check the 
> other lipids to make sure that there are no discrepancies in these.

> Also for my files I have included the bonded and non-bonded parameters 
> with parameters from CHARMM27 so as to allow simulations in water and 
> with proteins. I want to re-check these before contributing the 
> forcefield to the website, so it will probably be next week before I 
> upload it. Just to let you know I will use your lipids.rtp as it has the 
> atoms in separate charge groups so as to avoid having to use 
> -nochargegrp with pdb2gmx, whilst mine doesn't. I hope this is fine with 
> you.
For sure it is but you should be aware (and I think you are, since you were involved in the September discussion about this) that GROMACS does not treat charge groups as CHARMM does. See messages with subject "ARG Charmm gmx 4.5.1" (seems like the gmx-mailing list db is down so cannot provide you with a direct link). 


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