Hi Mark, Thank you for your reply. From your point of view, I wonder whether you mean I need to write a table based on different interaction types and then change the source code for recognition when running my case in the gromacs .I just have no idea about that .Can you give me further suggestion about that? I am stuck by this point
Thank you very much. Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL PROTECTED] Sent: Thursday, October 23, 2008 6:11 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions He, Yang wrote: > Hi all users, > > When I am defining the user potential functions using the table, I > encountered a problem that there are several unstable parameters in the > separate f(x),g(x),h(x) .For example, in the g(x), there is a parameter > "epsilon" whose value will depend on different pairs.In this situation, I can > not get a specific value in the table file . I don't know how to solve this > problem. > > Can anyone of you give me some suggestions about that? So your nonbonded interaction depends on your atom types. You could write a table for each interaction type, modify GROMACS to read them all in, and then modify the routine that calls the kernels to use the correct one. This additional memory usage would grow as the square of the number of atom types. You would also see some performance loss which you could minimize by arranging to evaluate all of one type of nonbonded interaction close together in the nonbonded routines, to minimize cache misses. Better would be if some of these functions (conveniently) differed only by a multiplicative or additive constant so that you could re-use the same table and then apply a correction function, but you'll have to look at your own maths for that. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users@gromacs.org 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
