I was using those "strange" values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small molecule. I was told to use those values but maybe it's not correct...
Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland ________________________________________ Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 17:20 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: > Pcoupl = Parrinello-Rahman > pcoupltype = semiisotropic > tau_p = 1.0 1.0e-14 > compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these bizarre values for tau_p and compressibility in the z-dimension? I recall another post where there was an issue of z-drift like this one. You're using a tau_p in the z-dimension of 1.0x10e-14 ps - I don't even see how that's possible! It is certainly far too strenuous for P-R coupling, where you should probably be using tau_p on the order of 5-10 ps. The compressibility also doesn't make any sense to me. 4.5e-5 in all dimensions should suffice. -Justin > ref_p = 1.0 1.0 -- ======================================== 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 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 -- 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
