[gmx-users] Hi...

[Navratna Vajpai]

Dear Eric..
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

*******************************************
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
	       +41 78 744 0810(M)

navratna.vajpai at unibas.ch



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