Fwd: [gmx-users] Hi...

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 14 22:10:57 CEST 2006

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. 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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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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