Re: [gmx-users] anisotropic pressure coupling for temperature annealing
Have you simulated the system without the annealing, to see if it does the same thing? Bilayers are very sensitive to minor changes in setup, using someone else's equilibrated bilayer coordinates doesn't mean it's equilibrated for your system. - Original Message From: Q733 [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, October 10, 2007 6:40:06 AM Subject: [gmx-users] anisotropic pressure coupling for temperature annealing Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. Any suggestion will be appreciated, thanks in advance. Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] anisotropic pressure coupling for temperature annealing
Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. Any suggestion will be appreciated, thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] anisotropic pressure coupling for temperature annealing
Q733 wrote: Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. tau_p and ref_p only take one parameter. The form for compressibility varies with pcoupletype. See manual section 7.3.14 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
