On Feb 2, 2011, at 11:48 AM, lloyd riggs wrote: > Dear Carsten Kutzner, > > First off, thanks. I did not specify it in the input md.mdp file, but when I > looked at the generated out.mdp it had a Linear center of mass removal for > the groups [system]. > > When I added the pull vector it works, untill the two subunits crash(move > past a realistic distance towards eachother and the force ==too much, and > then it crashes after atoms fly off....but I get a change in dG up untill > this point from solution. > > I will try and play around today, but woundered if anyone could spot check my > final .mdp input, as I lack in reviewers (for this portion of I or somebody else can take a quick look for any obvious issues, but nobody can guarantee the correctness of what you get, of course. This is entirely your responsibility.
Carsten > my work, ie people using gromacs). As at some distant point in time I will > try and publish dG/ dH and possibly dS, and relate these to affinities (Ka, > KD and kD), I would like to make sure I did it correctly before the hellish > number crunching(ie most time consuming) part. I did look over the tutorial > already... > > Thanks > > Stephan Watkins > > Message: 3 > Date: Tue, 1 Feb 2011 09:58:07 +0100 > From: Carsten Kutzner <[email protected]> > Subject: Re: [gmx-users] General MD question > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=iso-8859-1 > > Hi Stephan, > > On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote: > >> Dear All, >> >> A quick question as I have not really delved into code for gromacs ever, nor >> know anyone close whom has worked on it. >> >> If I set up an MD simulation using a 4 protein complex, and 1 small peptide, >> plus waters, etc...and run the whole thing the proteins never move, only the >> amino acids within(constant temp RT and pressure 1 bar). >> >> Two domains make one complex, and another two the other. Basically, if I >> seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will >> drift (the chains) towards each other, but the two large (global) protein >> units never move their center (I know I can make it work with Pull vectors, >> but why not in the simple system with a generated initial randomized >> velocities), I woundered why they are fixed in a normal run with minimal >> parameters? Is there a reason (specific to developers), historical reason, >> or other? As waters move around fine, and anything else added (salt, small >> molecules of 20-30 atoms, water) except the central molecule(s) of interest. > In a 'normal' run they should not be fixed. Could it be that you did > accidentally > fix them by specifying center of mass removal (comm-grps in .mdp)? > > Carsten > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
