We have tested virtual sites with CHARMM36 lipids; straightforward usage
gives too ordered membranes. We have created custom virtual sites
construction for lipid hydrogens and used them for pure membranes as well
as for membrane proteins, and the differences between membrane properties
with virtual sites and without are usually minor (but still noticeable).
The parameters can be found here http://memphys.dk/node/71 and the paper
http://pubs.acs.org/doi/abs/10.1021/ct500100f
Wojciech
Message: 1
Date: Mon, 29 Dec 2014 10:27:47 -0500
From: Justin Lemkul
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -vsite hydrogen
Message-ID: <54a172f3.5040...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote:
> Dear Users,
> I am simulating a membrane protein with charmm ff with a 2fs time step.
> How the results will be affected if I use a 5fs time step by using "-vsite
> hydrogen" option in pdb2gmx? Do my results loose their accuracy if I use
> this option?
Well, it's easy to test. The membrane properties that are expected to be
observed are very easy to quantify. We didn't test our CHARMM36 port with
virtual sites at all, so we cannot recommend such usage. Test thoroughly
before
doing any real production work. Membranes are extremely sensitive to
alteration.
-Justin
On Mon, Dec 29, 2014 at 8:52 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
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> Today's Topics:
>
>1. Re: -vsite hydrogen (Justin Lemkul)
>2. Re: Obtaining PMF for change in domain position (Justin Lemkul)
>3. pdb information (elham tazikeh)
>4. Re: pdb information (Justin Lemkul)
>5. Re: Obtaining PMF for change in domain position (Abhi Acharya)
>6. Gromacs error regarding default gromos bond type and angle
> type (Negar Parvizi)
>
>
> --
>
> Message: 1
> Date: Mon, 29 Dec 2014 10:27:47 -0500
> From: Justin Lemkul
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] -vsite hydrogen
> Message-ID: <54a172f3.5040...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote:
> > Dear Users,
> > I am simulating a membrane protein with charmm ff with a 2fs time step.
> > How the results will be affected if I use a 5fs time step by using
> "-vsite
> > hydrogen" option in pdb2gmx? Do my results loose their accuracy if I use
> > this option?
>
> Well, it's easy to test. The membrane properties that are expected to be
> observed are very easy to quantify. We didn't test our CHARMM36 port with
> virtual sites at all, so we cannot recommend such usage. Test thoroughly
> before
> doing any real production work. Membranes are extremely sensitive to
> alteration.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
>
> --
>
> Message: 2
> Date: Mon, 29 Dec 2014 10:29:18 -0500
> From: Justin Lemkul
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Obtaining PMF for change in domain position
> Message-ID: <54a1734e.5000...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/29/14 6:57 AM, Abhi Acharya wrote:
> > Hello GROMACS Users,
> >
> > This is a problem I am facing for the first time. Kindly guide be to the
> > best options.
> >
> > I have a protein which has two large domains connected by a flexible
> linker
> > peptide (~10 aa). The two domains seem to interact with each other and
> have
> > been crystallized in three different conformations. I want to calculate
> the
> > change in binding energy of the two domains wrt change in their relative
> > position, i.e. keeping position of one domain constant what is change in
> > binding energy as the other domain moves from conformation 1, through
> > conformation 2 to finally, conformation 3. What is the best way to do so?
> >
>
> You need to describe what these
