Fwd: [gmx-users] Hi...

[David van der Spoel]

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

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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