On 2012-10-15 03:10:18PM +0800, Jernej Zidar wrote: > The reason for using SPCE instead of TIP3P is that it performs way > better than TIP3P. This point is being emphasized everywhere along the > documentation. I will try simulating using TIP3P model. > > > > Is there a reason to switch water models? Gromacs supports both the > > traditional TIP3P and the CHARMM TIP3P (TIPS3P). > > > > Since you need to reinitialize velocities, it may not be a good idea to use > > Nose-Hoover and Parinello-Rahman straight away. Furthermore, you need > > to gen_vel=yes since gromacs has no velocity from your previous charmm run > > and subjecting an otherwise frozen system to a parinello-rahman thermostat > > is > > asking for trouble. > > gen_vel=yes does not seem to help
Have you tried just doing NVT with tcoupl = V-rescale and tau_t = 0.1 0.1? > > > > > Also, pressure coupling for NPT should probably be semiisotropic for > > bilayers. > > Finally you may want to experiment with EnerPres; see also > > http://pubs.acs.org/doi/abs/10.1021/ct3003157 (although this isn't related > > to > > your crash). > > EnerPres is already set. > > I tried your suggestions but the simulation still fails. > > Best, > Jernej Zidar > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
