As a follow up to my post (pasted below), I am providing some more details.
1. I am applying forces on heavy atoms (water oxygens and protein non-hydrogens). 2. I tried switching of SHAKE. Results improve marginally, but the 8 processor data are still wrong. 3. There is no pressure coupling. I have left a vapor layer of a few nanometers to allow for any density changes. I hope this further information helps in debugging. Thanks Sumanth Jamadagni Dear Gromacs community, I modified the pull code in GROMACS to apply forces on atoms that are in a certain region of space. It compiles error free and runs fine to give me the expected results. I then recompiled with mpi support. The cluster I am using has 8 cores/processors per node. When I use 1, 2 or 4 nodes to run, I get identical results, but the results are very different when I run parallel on all 8 cores. 1. I am not sure how the forces I apply in the pull code are parallelized. 2. Is this easy for me to edit in the source code or is it best if I use only upto 4 processors for my job? 3. Will the number of processors that I am able to use change depending on the system size? I currently have on protein and about 7500 water molecules to give a total of about 25000 atoms. I am using SHAKE with constraints on h-bonds. Thanks for any help! Sumanth Sumanth N Jamadagni Graduate Student Isermann Dept of Chemical and Biological Engg Rensselaer Polytechnic Institute jam...@rpi.edu (Cell)518-598-2786 http://boyle.che.rpi.edu/~sumanth -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
