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? 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