Fwd: [gmx-users] Hi...

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 14 15:36:47 CEST 2006

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 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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