Jelger Risselada wrote: > Finally had a look through the gromacs 4.0 source code. > Don't know if this bug/points already have been reported and changed in > 4.0.2: > > 1) There is never memory allocated for the pointers to the user defined > groups: > > mdatoms->cU1 etc.
I'm not sure, but there is a /* The user should fix this */ if (FALSE) srenew(md->cU1,md->nalloc); if (FALSE) srenew(md->cU2,md->nalloc); in ./src/mdlib/mdatom.c. You can remove the FALSE and get the memory allocation, I guess. Jochen > > These pointers will stay NULL when a user defined group is defined in > the mdp file. > I find these groups normally a pretty useful interface for simple fast > implementations. > > 2) The pull code has indeed completely changed, however to me the > questionable factor 0.5 remained the same: > In pull.c: > > /* Add the pull contribution to the virial */ > vir[j][m] += 0.5*f[j]*r_ij[g][m]; > > I do agree with the positive sign of the summation, but why is there a > factor 0.5 to correct for double counting included in the summation. The > summation is already ordered as r_ij and f[j] is the distance vector and > force between the particle and the equilibrium position of the spring > and therefore double counting cannot occur. Ofcourse it's possible that > this factor 0.5 is not meant as a double counting correction factor, but > then I don't see where it does come from. If this factor is indeed > incorrect it might affect the pressure significantly in case a large > pulling group is used. > > greetings > > Jelger > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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 > > . > -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ 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