RE: [gmx-users] settle issue
Thanks David, To switch on Dispersion Correction to the pressure will work ! Regards Yuguang Assist. Prof. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapore Tel: +65-63162885 email:ygmuATntu.edu.sg http://www.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, July 29, 2008 2:27 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] settle issue Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and seem to find a hint: in gromacs simulation the intra-molecular atom-atom distance (should be fixed by settle) fluctuation is quite large! How can one increase the accuracy of settles in gromacs? Settle is analytical and there is no tolerance. However you may be using settle with the SPC parameters (unlikely though). Maybe you should turn on the Dispersion Correction to the pressure (EnerPres). That gives a similar density difference. Regards Yuguang ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 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] settle issue
David van der Spoel wrote: Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and seem to find a hint: in gromacs simulation the intra-molecular atom-atom distance (should be fixed by settle) fluctuation is quite large! How can one increase the accuracy of settles in gromacs? Settle is analytical and there is no tolerance. However you may be using settle with the SPC parameters (unlikely though). Maybe you should turn on the Dispersion Correction to the pressure (EnerPres). That gives a similar density difference. Thanks, David. It works. With DispCorr=EnerPres, it gives 994. Regards Yuguang ___ 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 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] settle issue
Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and seem to find a hint: in gromacs simulation the intra-molecular atom-atom distance (should be fixed by settle) fluctuation is quite large! How can one increase the accuracy of settles in gromacs? Settle is analytical and there is no tolerance. However you may be using settle with the SPC parameters (unlikely though). Maybe you should turn on the Dispersion Correction to the pressure (EnerPres). That gives a similar density difference. Regards Yuguang ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
