> From: gromacs <ptf1...@163.com> > Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high
> Hi, > > I want to simulate 3x3x0.8 water film (bulk water) first creat the water, > > genbox -cs -o film.gro -box 3 3 0.8 > > then, i EM the bulk water; > > Using steep, but > > t = 0.011 ps: Water molecule starting at atom 298 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > > > then i run, and i get the result. I use NPT, and T=300K. I run several times, > but the final T was still 411K. > > > > So what could i do to get EM process successful? > > And what is the reason ? why i can not control the T 300K? > > > > Energy Average RMSD Fluct. Drift > Tot-Drift > ------------------------------------------------------------------------------- > Potential -9496.38 136.145 135.455 -0.158085 > -47.4256 > Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 > -8.45676 > Total Energy -7138.19 136.284 135.326 -0.186274 > -55.8824 > Temperature 411.945 12.8548 12.8477 -0.00492426 > -1.47728 > Pressure (bar) -1.66406 704.355 704.355 -0.00424907 > -1.27473 > Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 > -0.00233479 > Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 > -0.00233479 > Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 > -0.000622609 > Density (SI) 1038.7 13.6165 13.5998 0.00778513 > 2.33555 > Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) Hey, gromacs - Nice to hear from you here... It is a bad idea to simulate something with any cartesian dimension lower than a couple of nanometers using classical FFs. All your problems are generated by 0.8 nm of the z-side. -- Dr. Vitaly V. Chaban Rochester, U.S.A. -- 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
