Fwd: [gmx-users] Hi...

Dongsheng Zhang dong at pampas.chem.purdue.edu
Thu Sep 14 16:46:52 CEST 2006

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?

All the best!


>  What would be the "correct" 
> result anyway? Maybe your peptide unfolds.


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