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Today's Topics:
1. RE: g_sdf (Dallas B. Warren)
2. Membrane protein tutorial (Justin A. Lemkul)
3. distance restraints in Gromacs 4.0.4 (Ivan Gladich)
4. Pressure Coupling Problem (Joe Joe)
5. Pressure Coupling Problem (chris.ne...@utoronto.ca)
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Message: 1
Date: Wed, 08 Apr 2009 09:41:44 +1000
From: "Dallas B. Warren" <dallas.war...@pharm.monash.edu.au>
Subject: RE: [gmx-users] g_sdf
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<89907ea1dcfb7548a431c13a270f9dd507019...@prk-exch-01.vcp.local>
Content-Type: text/plain; charset=us-ascii
What exactly your issue with using g_sdf?
You need to supple a trajectory, index, and topology. Index contains
the three reference atoms for the molecule, plus the atom you are
calculating the sdf to. Selection of the correct grid size and binwidth
is required to get something that looks as you want it.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
------------------------------
Message: 2
Date: Tue, 07 Apr 2009 19:55:28 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: [gmx-users] Membrane protein tutorial
To: "Gromacs Users' List" <gmx-users@gromacs.org>
Message-ID: <49dbe7f0.4040...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello all,
Due to the recent influx in questions related to membrane proteins (especially
with common questions), I decided to put together a step-by-step tutorial for
membrane protein systems. It's a work in progress, so I would genuinely
appreciate feedback from anyone who has a few minutes to take a look. These
procedures make sense in my head, so hopefully that comes through in the
instructions :)
I have posted a link on the wiki site to my tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I hope that people find this useful. I have attempted to walk the user through
most practical concerns that arise regarding topology organization and a few
analysis questions that show up on the list frequently (g_order, g_density, etc).
If you have comments or questions, please do not hesitate to send me a private
message.
-Justin
Thanks Justin for this effort, This is a great job.
Stefane
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