Dear GROMACS users, I am hoping to get some information from you experts regarding the use of user-defined potentials (table*.xvg). With the help of the GROMACS manual and several posts in the mailing list, I have been able to make user-defined potential functions that I would like to apply to a system of small molecules (16 atoms each, ~100 molecules). The crux of the problem (see below) is that I would like to apply **separate** user-defined potentials for *intra* and *inter* molecular interactions **in a computationally efficient way**. The molecule I'm simulating (in united-atom representation) is:
C1 - O1 - C - C - O2 - C2 and I want: (1) a user defined potential applied between C1 and C2 on the same molecule (2) a different user defined potential between C2 and O1 (& C1 and O2) on the same molecule (3) a normal gromacs table potential applied between C1 and C2 on *different* molecules (4) a normal gromacs table potential applied between C2 and O1 (also C1 and O2) on *different* molecules I can do this by defining a large number of 'energygrps'; specifically I need 4 different 'energygrps' for each molecule (i.e. separate ones for 'C1', 'C2', 'O1', & 'O2', with all other atoms lumped into a single 'energygrp' for all molecules). Because my simulation system currently contains 91 molecules this results in 365 'energygrps' in the *.mdp file. Since this is a lot of 'energygrps' I redimensioned the gromacs arrays in order to handle it as noted previously in the mailing list: http://www.gromacs.org/pipermail/gmx-users/2007-October/030084.html This works great but **here's the problem** : the simulations run exceedingly slow when I use such a high number of defined 'energygrps'. Without using the user defined potential functions I was getting roughly 25 ns/day (which, as always with GROMACS, is amazingly fast!). With the applied potential functions and 'energygrps' however I am only getting 1.5 ns/day. I thought one problem might be the number of times that 'mdrun' spends writing to the energy (.edr) file, but I have ruled this out as a possibility because when I increased my 'nstenergy' in my *.mdp file by 100 fold 'mdrun' still runs at the same slow rate. The slowdown therefore appears to be directly related to the number of 'energygrps.'. To confirm this, I decreased the number of 'energygrps' to 3 (by lumping all 'C1' and 'C2' atoms together into one 'energygrp' and all 'O1' and 'O2' atoms into another 'energygrp') and this accelerated the simulations dramatically; however, the same user defined potential functions are then applied to both **intra** and **inter**molecular interactions, which is not what I want! If anyone has any suggestions for speeding up the simulations I'd really appreciate hearing from you! Thanks in advance for your help. Any and all comments are appreciated :) Eli Musselman _______________________________________________ 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
