On Sat, Mar 23, 2013 at 7:25 PM, Shima Arasteh <[email protected]>wrote:
> That's right. > But I' d like to be sure about this fact that both restraints are applied. > I see just 1 position restraints energy term in log file. Is just > visualizing the trr file the only way of becoming sure that the headgroups > and protein are restrained? > You can use the -pp flag with grompp to get a post-processed stand-alone .mdp file that might illustrate what you wish to confirm. Otherwise, gmxdump -s your.tpr will definitely have the information (but piecing together the indexing to show which atoms have position restraints can be painful). And one more question is that, to eliminating the position restraints in > MDRUN, is it supposed to reduce the force on atoms before mdrun gradually? > Or it is ok to reduce it in MD step? > You can do whatever you like by varying the force constant between runs, but an individual run will be on or off. Mark -- 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
