Dear David,
Thanks again for your advice. This is just a very crude idea to restrain the water's orientation close to protein surface. I am just curious to see, how the rotation and translation play a role during the solvation process respectively. I did a literature search, but didn't see the similar work. I am even not sure if the "orientation restrain" is possible now. Is there something else in gromacs which can do the similar thing? Tanping --- David Mobley <[EMAIL PROTECTED]> wrote: > Tanping, > > > Thanks for your attention. I want to restrain the > > water's orientation close to protein surface. I > have > > two problems: > > > > * what is a good reference group for the > orientation? > > * The orire_fc value. > > > > Is orientational restraints the proper function I > > should use? Thank you again for your nice help. > > I don't know and have no experience with this. > However, in terms of > general advice, when you ask for a specific value > for something (i.e. > the orientational restraints force constant) you > probably want to > explain what exactly you want a force constant for, > as one would > obviously use a very different force constant to > restrain a water > molecule than a protein. > > Otherwise, all I can say is try and find other work > that has > restrained water orientations, and look to see what > they've done and > whether it worked well. I am not too clear on why > you would want to do > this. > > David > > > > > > > Tanping > > > > > > > > --- David Mobley <[EMAIL PROTECTED]> wrote: > > > > > What are you trying to use orientational > restraints > > > to restrain? > > > Ordinarily, you probably don't want such > restraints, > > > hence the default > > > value is zero. > > > > > > On 7/25/06, Tanping Li <[EMAIL PROTECTED]> > wrote: > > > > Hellow everyone, > > > > > > > > I notice that the default value for > orire_fc=0, > > > which > > > > set the orientation restrain as the none. What > is > > > the > > > > reasonable value for the orire_fc? Any > suggestion > > > will > > > > be greatly appretiated. Thanks a lot! > > > > > > > > > > > > Best > > > > Tanping > > > > > _______________________________________________ > > > > gmx-users mailing list > gmx-users@gromacs.org > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > > 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 > > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > 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 > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
