| 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) |
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
