Dear Chris Neale, I wanted to generate directed initial velocities for two seperate multiprotein complexes, but just so they start to move through the void towards each other. The only way I found to do this was to use the COM pulling, but then it is a "biasing" force applied across the entire MD sim. Basically I want to minimize the bias, if possible, but was asking if there is a way to apply an initial directional (instead of the random)velocity/force without a constant applied force like the COM pulling. If it is the only way, I can do the calculations with COM pulling and correct for my applied force, but was hopeing there was another way I did not find which would be more simple, or just something I missed.
In Solvent, the complexes move (albeit random), and one only need to let it run long enough, or apply walls, but in vacuo if there is no applied force, the atoms within the complexes move around, but not the molecules as a whole, they just sit waving at each other across a void. As they are in a void however, an initial force would not dissapate until the two larger molecules connected, so I am woundering if there would even be a difference between what I wanted, and general COM pulling. reguardless,thanks for any reply. Sincerely, Stephan Watkins ------------------------------ Message: 4 Date: Wed, 15 Dec 2010 11:04:12 -0500 From: chris.ne...@utoronto.ca Subject: [gmx-users] Com Pulling To: gmx-users@gromacs.org Message-ID: <20101215110412.imqto29twk8ks...@webmail.utoronto.ca> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" If I understand correctly, you want to apply a biasing force and you also want to have an "unbiased" simulation. These two things are not possible in combination. There are a variety of techniques available that will give you particular information. For example, you can extract the unbiased PMF from umbrella sampling (but not the unbiased dynamics); you can also study some things with reaction path sampling or slow AFM pulling, but for us to help you you will need to describe what you want to do. Chris. -- original message -- Dear All, I was setting up things to use COM pulling for a multiprotein complex. My question after going through the gromacs documentation(online) is: Is there a way to limit either the time or distance two groups are pulled towards each other(reguarding only the applied force), as I could not find anything. Basically, if I run something in vacuo, the groups (proteins) do not move globally even when constraints, etc are set to none. To measure any Gibbs , delta H etc...I need the groups too move towards each other and form the interactions I am measuring, but do not want the pull force to interfear with overall calculations. My thoughts were to do a very short run, and then either remove the pull force, etc from the .mdp file, and use a checkpoint to re-start it, but do not know if this would work or would maintain the movement however arbitrary in the general correct direction. that or use such a small (.2 kcal/mol nm2) that it does not matter very much. Sincerely, Stephan Watkins -- Sicherer, schneller und einfacher. Die aktuellen Internet-Browser - jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists