[gmx-users] Hi...

Navratna Vajpai navratna.vajpai at unibas.ch
Thu Sep 14 15:50:05 CEST 2006

Sorry for not so explicitly explaining the things.. Here it goes
I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field.
when I used the OPLS-AA the phi angles came out to be -ve for three  
of the amino acids. which is stericaly not allowed. But when I ran it  
using GROMOS I found all the phi-psi combinations with a negative phi  
value distribution. But now I am lost as you have said it works only  
for GROMOS like force field. Why?
and if that so I have got -ve phi distribution for the other phi-psi  
My other question remained unanswered even now. Is there any way  
really to judge which force field is to be chosen for particular type  
of analysis?
Best regards

On Sep 14, 2006, at 3:36 PM, 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. 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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Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
Basel, Switzerland.
Phone- +41 61 267 2080(O)
	       +41 78 744 0810(M)

navratna.vajpai at unibas.ch

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