On Thu, 2006-09-14 at 13:10 -0700, David van der Spoel wrote: > Dongsheng Zhang wrote: > > On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: > >> Navratna Vajpai wrote: > >>> Hi all.. > >>> I wrote this mail yesterday. But could not receive any reply till now. > >>> So if someone can suggest something about it. That would be nice. > >>> Best regards > >>> Nav > >>> > >>> Begin forwarded message: > >>> > >>>> *From: *Navratna Vajpai <[EMAIL PROTECTED] > >>>> <mailto:[EMAIL PROTECTED]>> > >>>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00 > >>>> *To: *Discussion list for GROMACS users <gmx-users@gromacs.org > >>>> <mailto:gmx-users@gromacs.org>> > >>>> *Subject: **[gmx-users] Hi...* > >>>> *Reply-To: *Discussion list for GROMACS users <gmx-users@gromacs.org > >>>> <mailto:gmx-users@gromacs.org>> > >>>> > >>>> Dear All > >>>> Hi.. > >>>> This is in regard to your previously replied mail regarding the use of > >>>> GROMOS96 or OPLS-AA or AMBER force field. > >>>> As you said it depends upon the users taste which one to use. This > >>>> means that the three on a broad manner should give convergence of > >>>> the analyzed data set. > >>>> Infact from my simulation runs using oplss-aa and gromos96, I didn't > >>>> found that. I tried using the GROMOS96 and opls-aa force field on my > >>>> small peptides for a period of 20ns and found that with opls-aa even > >>>> the phi-psi combination of the individual amino acids were incorrect. > >>>> Actually this always puzzled me to make a choice for the Force field. > >>>> The rest of the script was unchanged for the two runs. > >>>> Could you please comment on the above results? Is there any way really > >>>> to judge which force field is to be chosen for particular type of > >>>> analysis? > >>>> Best regards > >>>> Nav > >>>> > >> > >> what do you mean with incorrect? your question is quite vague. > >> > >> the g_rama program works only for GROMOS like force fields unfortunately > >> but that doesn't mean the phi/psi are wrong. > > > > Could you please give more detail why g_rama program works only for > > GROMOS like force field? To my understanding, the reason to get > > different values of phi/psi by using g_rama or g_angle is that the > > definition of phi/psi in g_rama is not in a conventional way. If we > > define phi/psi in the same way as g_rama, I believe g_angle will give > > the same answer. No matter which force field is used, these two methods > > will give different values. Is my understanding correct? > > > because atom names are hardcoded. So you mean, atom names in g_rama is consistent with gromos like FF, not others. If so, could you please add this documentation in g_rama -h. Thank you very much for your clarification.
All the best! Dongsheng > if you give g_angle the right > definitions in the index file it will work correctly. > > > > All the best! > > > > > > Dongsheng > > > > > >> What would be the "correct" > >> result anyway? Maybe your peptide unfolds. > > > > _______________________________________________ > > 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
