Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information?
Thanks, Shuangxing Dai On Jul 12, 2010, at 15:43, "Justin A. Lemkul" <[email protected]> wrote: > > > Shuangxing Dai wrote: >> Hi, all: >> I am studying thermal expansion of bulk crystal solid. I want to reach >> the state with 300K in temperature and 1 bar pressure. I am not sure >> whether my procedure is correct or not. >> First I run energy minimization, then a constant volume for temperature >> coupling ( integrator is sd), then run with Berendson for anisotropic >> pressure coupling for 50 ps, then run anisotropic pressure coupling using >> Panello-Rahman for 10 ps, finally a constant volume step for production for >> 10 ps. >> I do not know whether this procedure is correct or not. Also, since for >> my small system, fluctuation is very large, so is there any way to reach the >> state ( 300K and 1 bar) and the system is fully in equilibrium? > > The timeframes you're using are extremely short. I'd suspect that it would > be hard to get any system, especially a small one prone to large > fluctuations, in an equilibrium state in 70 ps total. Simple equilibration > of a protein in water is typically done for no less than 100 ps per ensemble. > >> Also, I got a question about the ,mdp file options. When I use md >> integrator, with Nose-Hover for temperature coupling and Panello-Rahman >> pressure coupling, there is no error information. When I change and use >> Berendson for pressure coupling, there is error information and does not >> work. > > Well, what's the error? This kind of description will get you no useful > advice. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. > > -Justin > >> Anyone have idea about these? Thanks in advance. >> Thanks, >> Shuangxing Dai > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
