Hi For running simulaion parameters, people normally not write the details in their papers.
high-temperature (up to 600 K) simulations of proteins in TIP3P...... any other detailed suggestion about this ? Thank you Lin I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the water model is TIP3P. > > Thanks > Lin > > > > I think the problem is hidden in your water force field model. > > > > The simulation system is merely water + one lysozyme. > > I increase temperate to 550K. > > > > Then, the simulation broke. > > The following message is shown. > > > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > > mpiexec: Warning: task 0 exited with status 1. > > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > > > > Anything wrong with the simulation? > > > > Thank you > -- 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
