One a system passes EM and a couple of ps of MD, is it always stable indefinitely? If not, then something is wrong somewhere.
-- original message -- Dear Chris, I put one tip5p molecule in a center of dodecahedral box - 2nm from that molecule to walls, filled it with tip5p, ran 6000 steps of steep minimization. After another 2704 steps of cg it converged to emtol 1.0. I run 100k steps of nvt on this box afterwards (http://shroom.ibb.waw.pl/tip5p/pure1). But the water is very capricious. If I ran only 2000 steps of steep, the following cg crashed after less than 1000 steps because a water molecule could not be settled. I could not minimize another box, filled only by genbox from an empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand that you have to have some luck if you run a simulation in pbc with rigid water, which interacts through walls of the box with the other side and was not well placed. Also, I had several segfaults during minimization that I was able to avoid only by limiting the number of cores. I checked distances between OW and LPx on a crashing minimization with a peptide - 2812 water molecules. Maximum force reached 8.8e+24 in 225 steep steps, but all the 5624 distances were rock solid 0.7A, as expected. I still did not post the redmine issue, I want to be sure that I am doing everything correctly. On 2013-09-29 18:47, Christopher Neale wrote: > Dear Grzegorz: > > Under no conditions should any of the tip5p geometry change (for the > standard tip5p model). > If you find that this is happening, then that is certainly an error. > You can check if you like by analyzing > your trajectory. However, flexible bonds will allow the distance from > the arginine N to the arginine > H to vary, which my allow a closer approach of the arginine H to the > tip5p dummy site. > > Did you verify that a water box (no protein) simulates without error? > > Did you post a redmine issue with .mdp , .gro , and .top files? > > Chris. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists