Fwd: [gmx-users] Hi...

[Dongsheng Zhang]

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 <navratna.vajpai at unibas.ch 
> >>>> <mailto:navratna.vajpai at unibas.ch>>
> >>>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00
> >>>> *To: *Discussion list for GROMACS users <gmx-users at gromacs.org 
> >>>> <mailto:gmx-users at gromacs.org>>
> >>>> *Subject: **[gmx-users] Hi...*
> >>>> *Reply-To: *Discussion list for GROMACS users <gmx-users at gromacs.org 
> >>>> <mailto:gmx-users at 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.
> > 
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