Dear Mark, thanks for your reply! I'll try to better focus my issue: my intent is to perform simulations similar to which described in some recently published papers in which cavities are expanded by means of LJ spheres, using methods called "pressure guided MD" or "active-site pressurization" (Kimura et al., Proteins 2008 Jan 3; Mazanetz et al., Biochemical Society Transactions 2008). I'm working with a receptor model but experimental informations about the ligand binding mode are not available to date. I don't want to introduce bias in my MD simulations using a structure with the ligand already inserted so, inspired by that papers, I was thinking about LJ spheres. How can I apply this approach with gromacs?
Chiara On Feb 19, 2008 2:06 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Chiara Parravicini wrote: > > Hi Mark, > > > > I just want make use of the volumes of the spheres to enlarge the pocket > > without the use of any ligands. > > How about using a ligand with charges set to zero? Or that and > tinkered-LJ parameters? > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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