> Dear Gromacs users, > > I'd like to perform a simulation following the protocol applied in the > Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor. > Ligand > docking and identification of a putative binding site of the distal hexose > moiety.* *Bioorg. Med Chem Lett.* 2007;17(3):761-6. ). > > In particular, I refer to some topic details reported here: > > *...The MD simulation was performed using [...] CHARMM 32a216 [...] 15 > attempts to generate a MD trajectory without applying nuclear Overhauser > enhancement (NOE) restraints led to a loss of the secondary structure of > TM7. For this reason the first 5 ns of the MD were performed with the NOE > restraints applied for the distances between the backbone carbonyl oxygen > atom of the residue n and the backbone NH-group of the residue n+4 of > TM7[...]The restraints were applied to all the residues, with the > exception > of the prolines and residues immediately following [...]That constraint > preserved the helical structure of TM7, which remained stable after > removing > the NOE restraints. [...] After 5 ns the MD simulation was continued > without > any restraints...* > > How can I do it with Gromacs? > > I suppose that I also could manually provide classical distance > restraints, > defining arbitrary Hbond cutoffs instead of NOE distance restraints, but a > such alternative sounds less elegant to me.
There's a whole section in the manual on such restraints. Please start by reading there and come back with specific questions. 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
