David, Thanks for your reply.
I am currently using 3.3.1 code. I am increase the force, to be able to calculate the free energy required of introducing the angle restraints in the system. I use small force increments each run, using a delta_lambda of 0. Decreasing or increasing in my view only changes the sign of the overall graph, but it should not allow dG/dl to cross zero. Thanks, Maarten > > From: "David Mobley" <[EMAIL PROTECTED]> > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Thu, 11 May 2006 09:34:28 -0700 > Subject: Re: [gmx-users] angle restraints > > Maarten, > > What version of the code are you using? There was a bug in the angle > restraints code until 3.3.1 (or 3.3 cvs) which caused angle > restraints > to turn off gradually as a function of lambda in free energy > calculations, if I remember correctly. (See bugzilla for details: > http://bugzilla.gromacs.org/show_bug.cgi?id=43). > > However, I'm not sure that relates to the problem you're describing, > but it probably does, depending on the version you are using. > > What exactly are you changing in the free energy calculation? Are you > changing the angle restraint as a function of lambda? If so, which > way > are you changing it? Decreasing or increasing restraints? > > David > > > > On 5/11/06, Maarten Wolf <[EMAIL PROTECTED]> wrote: > > Dear users, > > > > I have a small system with a number of small peptides. I want to > > constraint the angle between the N-term to C-term vectors of > different > > peptides. This works well, but if I do a FEP calculation the dG/dl > > becomes smaller than zero at some point. > > I expected it to be at least allways greater than zero (zero in the > > limit that the restraint does not have to do anything), since a > force > > has to be aplied to restraint the angles. > > Can anybody explain where I am going wrong? > > > > Thanks > > Maarten > > > > Send instant messages to your online friends > http://uk.messenger.yahoo.com > > _______________________________________________ > > 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 > MvG Maarten ****************************************************** ** Work Adress Julianalaan 136 ** ** 2628 BL Delft ** ** Netherlands ** ** +31(0)15-2789382 ** ****************************************************** ___________________________________________________________ Switch an email account to Yahoo! Mail, you could win FIFA World Cup tickets. http://uk.mail.yahoo.com _______________________________________________ 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