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 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
