Hi David,
Thank you for your reply. As for the new non-bond potential, if I want to use the gromacs to deal with them, what should i do in the gromacs? Do you have any suggestions about that? Change the source code? Thank you for your help. Regard, Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of David van der Spoel [EMAIL PROTECTED] Sent: Tuesday, October 21, 2008 11:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] modify bondfree.c and recompile He, Yang wrote: > Hi Jian, > > Do you also need to change the source code to get a new potential function? I > am also engaged in this job. DO you have any experience about this job? > > You can use tables for bonded potentials as well, without changing any code. > Regards, > > Yang > ________________________________________ > From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL > PROTECTED] > Sent: Tuesday, October 21, 2008 7:24 AM > To: [EMAIL PROTECTED]; [email protected] > Subject: [gmx-users] modify bondfree.c and recompile > > Hi, > > If I only change some functional form in bondfree.c (the number of > parameters are kept the same), can I just do "make mdrun" and "make > install-mdrun" to recompile from the source? > > I cannot find the dependency between the source files and the Gromacs > utilities (grompp and mdrun). > > I compare the tpr file generated before and after the change and they > are the same. Therefore it seems to me that grompp does not read the > formulation of bonded interactions, am I right? > > Thank you very much for the reply. > > > Regards, > > Jian > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 -- David. ________________________________________________________________________ David van der Spoel, PhD, Professor of Biology 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
