gmx-users http://www.mail-archive.com/gmx-users@gromacs.org gmx-users @ gromacs Sat, 11 Feb 2012 00:22:39 GMT Sat, 11 Feb 2012 00:22:39 GMT http://blogs.law.harvard.edu/tech/rss MHonArc RSS 2.0 RCFile themailarchive@gmail.com (The Mail Archive) The Mail Archive http://www.mail-archive.com/nanologo.png http://www.mail-archive.com/gmx-users@gromacs.org [gmx-users] g_wham with cylinder geometry http://www.mail-archive.com/gmx-users@gromacs.org/msg47769.html <font color=#6f6f6f> 2012/02/11</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22MPID%22">MPID</a> Sat, 11 Feb 2012 00:22:35 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47769.html Re: [gmx-users] improper dihedral angle in charmm and opls aa http://www.mail-archive.com/gmx-users@gromacs.org/msg47768.html <font color=#6f6f6f> 2012/02/11</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Sat, 11 Feb 2012 00:15:36 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47768.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47767.html <font color=#6f6f6f> 2012/02/11</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Sat, 11 Feb 2012 00:12:00 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47767.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47766.html <font color=#6f6f6f> 2012/02/11</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Sat, 11 Feb 2012 00:09:18 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47766.html [gmx-users] improper dihedral angle in charmm and opls aa http://www.mail-archive.com/gmx-users@gromacs.org/msg47765.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Tom%22">Tom</a> Fri, 10 Feb 2012 22:54:17 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47765.html Re: [gmx-users] SWM4-NDP WATER MODEL AND IONS http://www.mail-archive.com/gmx-users@gromacs.org/msg47764.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Abhijeet Joshi%22">Abhijeet Joshi</a> Fri, 10 Feb 2012 22:19:55 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47764.html Re: [gmx-users] SWM4-NDP WATER MODEL AND IONS http://www.mail-archive.com/gmx-users@gromacs.org/msg47763.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22David van der Spoel%22">David van der Spoel</a> Fri, 10 Feb 2012 22:11:38 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47763.html Re: [gmx-users] SWM4-NDP WATER MODEL AND IONS http://www.mail-archive.com/gmx-users@gromacs.org/msg47762.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Abhijeet Joshi%22">Abhijeet Joshi</a> Fri, 10 Feb 2012 21:55:54 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47762.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47761.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Fri, 10 Feb 2012 17:15:44 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47761.html [gmx-users] Npt equilibration of the membrane-mimicking, CCl4 layer http://www.mail-archive.com/gmx-users@gromacs.org/msg47760.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Thomas Schlesier%22">Thomas Schlesier</a> Fri, 10 Feb 2012 16:52:28 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47760.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47759.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Fri, 10 Feb 2012 15:48:45 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47759.html Re: [gmx-users] DMPC diffusion: G54A7 http://www.mail-archive.com/gmx-users@gromacs.org/msg47758.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22David van der Spoel%22">David van der Spoel</a> Fri, 10 Feb 2012 15:19:58 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47758.html [gmx-users] DMPC diffusion: G54A7 http://www.mail-archive.com/gmx-users@gromacs.org/msg47757.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Jon Kapla%22">Jon Kapla</a> Fri, 10 Feb 2012 15:15:07 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47757.html [gmx-users] Re: genbox - Umbrella Sampling http://www.mail-archive.com/gmx-users@gromacs.org/msg47756.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Steven Neumann%22">Steven Neumann</a> Fri, 10 Feb 2012 15:00:52 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47756.html [gmx-users] genbox - Umbrella Sampling http://www.mail-archive.com/gmx-users@gromacs.org/msg47755.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Steven Neumann%22">Steven Neumann</a> Fri, 10 Feb 2012 14:55:14 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47755.html Re: [gmx-users] Shift functions http://www.mail-archive.com/gmx-users@gromacs.org/msg47754.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Fri, 10 Feb 2012 14:41:53 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47754.html Re: [gmx-users] Shift functions http://www.mail-archive.com/gmx-users@gromacs.org/msg47753.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Elisabeth%22">Elisabeth</a> Fri, 10 Feb 2012 14:19:52 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47753.html Re: [gmx-users] Shift functions http://www.mail-archive.com/gmx-users@gromacs.org/msg47752.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22aldi asmadi%22">aldi asmadi</a> Fri, 10 Feb 2012 14:00:22 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47752.html Re: [gmx-users] Shift functions http://www.mail-archive.com/gmx-users@gromacs.org/msg47751.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Fri, 10 Feb 2012 13:58:33 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47751.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47750.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Fri, 10 Feb 2012 13:53:45 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47750.html [gmx-users] Shift functions http://www.mail-archive.com/gmx-users@gromacs.org/msg47749.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Elisabeth%22">Elisabeth</a> Fri, 10 Feb 2012 13:53:06 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47749.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47748.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Fri, 10 Feb 2012 13:41:58 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47748.html Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer http://www.mail-archive.com/gmx-users@gromacs.org/msg47747.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Fri, 10 Feb 2012 12:59:51 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47747.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47746.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Fri, 10 Feb 2012 12:59:16 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47746.html [gmx-users] Re: Using shell script to analyze the results http://www.mail-archive.com/gmx-users@gromacs.org/msg47745.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Kathleen Kirchner%22">Kathleen Kirchner</a> Fri, 10 Feb 2012 12:23:50 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47745.html Re: [gmx-users] Using shell script to analyze the results http://www.mail-archive.com/gmx-users@gromacs.org/msg47744.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Kiwoong Kim%22">Kiwoong Kim</a> Fri, 10 Feb 2012 12:17:00 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47744.html Re: [gmx-users] Using shell script to analyze the results http://www.mail-archive.com/gmx-users@gromacs.org/msg47743.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Nuno Azoia%22">Nuno Azoia</a> Fri, 10 Feb 2012 12:07:31 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47743.html Re: [gmx-users] Using shell script to analyze the results http://www.mail-archive.com/gmx-users@gromacs.org/msg47742.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22shahid nayeem%22">shahid nayeem</a> Fri, 10 Feb 2012 11:55:19 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47742.html Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer http://www.mail-archive.com/gmx-users@gromacs.org/msg47741.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22James Starlight%22">James Starlight</a> Fri, 10 Feb 2012 11:09:04 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47741.html [gmx-users] Using shell script to analyze the results http://www.mail-archive.com/gmx-users@gromacs.org/msg47740.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Kiwoong Kim%22">Kiwoong Kim</a> Fri, 10 Feb 2012 10:50:19 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47740.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47739.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Fri, 10 Feb 2012 10:29:23 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47739.html Re: [gmx-users] how to get the block averaged MSD curve ? http://www.mail-archive.com/gmx-users@gromacs.org/msg47738.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22David van der Spoel%22">David van der Spoel</a> Fri, 10 Feb 2012 09:44:23 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47738.html Re: [gmx-users] how to get the block averaged MSD curve ? http://www.mail-archive.com/gmx-users@gromacs.org/msg47737.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Tsjerk Wassenaar%22">Tsjerk Wassenaar</a> Fri, 10 Feb 2012 09:36:03 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47737.html Re: [gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model http://www.mail-archive.com/gmx-users@gromacs.org/msg47736.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Fri, 10 Feb 2012 07:26:17 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47736.html Re: [gmx-users] Re: REMD tutorial http://www.mail-archive.com/gmx-users@gromacs.org/msg47735.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Fri, 10 Feb 2012 07:21:05 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47735.html Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47734.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Fri, 10 Feb 2012 07:15:38 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47734.html [gmx-users] Check out my photos on Facebook http://www.mail-archive.com/gmx-users@gromacs.org/msg47733.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Wara Ell Boon%22">Wara Ell Boon</a> Fri, 10 Feb 2012 06:30:56 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47733.html Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47732.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22vivek sharma%22">vivek sharma</a> Fri, 10 Feb 2012 05:41:38 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47732.html Re: [gmx-users] Problem with simulation of Protein-DNA complex http://www.mail-archive.com/gmx-users@gromacs.org/msg47731.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Tsjerk Wassenaar%22">Tsjerk Wassenaar</a> Fri, 10 Feb 2012 05:08:35 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47731.html [gmx-users] Re: REMD tutorial http://www.mail-archive.com/gmx-users@gromacs.org/msg47730.html <font color=#6f6f6f> 2012/02/10</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22bharat gupta%22">bharat gupta</a> Fri, 10 Feb 2012 02:20:28 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47730.html [gmx-users] Equilibration of polymer chains- gauche defects http://www.mail-archive.com/gmx-users@gromacs.org/msg47729.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Elisabeth%22">Elisabeth</a> Thu, 09 Feb 2012 23:41:19 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47729.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47728.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Thu, 09 Feb 2012 18:42:29 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47728.html [gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model http://www.mail-archive.com/gmx-users@gromacs.org/msg47727.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22GZ Zhang%22">GZ Zhang</a> Thu, 09 Feb 2012 18:11:58 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47727.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47726.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Thu, 09 Feb 2012 18:07:33 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47726.html Re: [gmx-users] Using groups in the mdp file http://www.mail-archive.com/gmx-users@gromacs.org/msg47725.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Ignacio Fernández Galván%22">Ignacio Fernández Galván</a> Thu, 09 Feb 2012 17:05:09 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47725.html Re: [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47724.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Thu, 09 Feb 2012 16:42:40 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47724.html [gmx-users] Energy minimization Error http://www.mail-archive.com/gmx-users@gromacs.org/msg47723.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Thu, 09 Feb 2012 16:06:31 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47723.html Re: [gmx-users] Error energy minimization on protein with implicit water http://www.mail-archive.com/gmx-users@gromacs.org/msg47722.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22aiswarya pawar%22">aiswarya pawar</a> Thu, 09 Feb 2012 13:09:33 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47722.html Re: [gmx-users] Problem with simulation of Protein-DNA complex http://www.mail-archive.com/gmx-users@gromacs.org/msg47721.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22rarora%22">rarora</a> Thu, 09 Feb 2012 13:09:14 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47721.html Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47720.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Thu, 09 Feb 2012 13:06:08 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47720.html Re: [gmx-users] Error energy minimization on protein with implicit water http://www.mail-archive.com/gmx-users@gromacs.org/msg47719.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Thu, 09 Feb 2012 13:03:43 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47719.html [gmx-users] Error energy minimization on protein with implicit water http://www.mail-archive.com/gmx-users@gromacs.org/msg47718.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22aiswarya pawar%22">aiswarya pawar</a> Thu, 09 Feb 2012 13:02:19 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47718.html Re: [gmx-users] Error energy minimization on protein with implicit water http://www.mail-archive.com/gmx-users@gromacs.org/msg47717.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22lina%22">lina</a> Thu, 09 Feb 2012 12:58:49 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47717.html Re: [gmx-users] how to get the block averaged MSD curve ? http://www.mail-archive.com/gmx-users@gromacs.org/msg47716.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22lina%22">lina</a> Thu, 09 Feb 2012 12:56:52 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47716.html Re: [gmx-users] Problem with simulation of Protein-DNA complex http://www.mail-archive.com/gmx-users@gromacs.org/msg47715.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22lina%22">lina</a> Thu, 09 Feb 2012 12:52:45 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47715.html [gmx-users] Problem with simulation of Protein-DNA complex http://www.mail-archive.com/gmx-users@gromacs.org/msg47714.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22rarora%22">rarora</a> Thu, 09 Feb 2012 12:45:11 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47714.html [gmx-users] how to get the block averaged MSD curve ? http://www.mail-archive.com/gmx-users@gromacs.org/msg47713.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Kiwoong Kim%22">Kiwoong Kim</a> Thu, 09 Feb 2012 11:26:24 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47713.html [gmx-users] All-bonds vs h-bonds contraints http://www.mail-archive.com/gmx-users@gromacs.org/msg47712.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22gpat%22">gpat</a> Thu, 09 Feb 2012 10:23:28 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47712.html [gmx-users] Error energy minimization on protein with implicit water http://www.mail-archive.com/gmx-users@gromacs.org/msg47711.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22aiswarya pawar%22">aiswarya pawar</a> Thu, 09 Feb 2012 10:18:32 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47711.html [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47710.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22vivek sharma%22">vivek sharma</a> Thu, 09 Feb 2012 06:02:48 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47710.html [gmx-users] Feller DOPC coordinates http://www.mail-archive.com/gmx-users@gromacs.org/msg47709.html <font color=#6f6f6f> 2012/02/09</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22MPID%22">MPID</a> Thu, 09 Feb 2012 00:34:49 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47709.html Re: [gmx-users] g_x2top http://www.mail-archive.com/gmx-users@gromacs.org/msg47708.html <font color=#6f6f6f> 2012/02/08</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22David van der Spoel%22">David van der Spoel</a> Wed, 08 Feb 2012 21:56:35 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47708.html [gmx-users] g_x2top http://www.mail-archive.com/gmx-users@gromacs.org/msg47707.html <font color=#6f6f6f> 2012/02/08</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Andrew DeYoung%22">Andrew DeYoung</a> Wed, 08 Feb 2012 21:36:55 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47707.html Re: [gmx-users] How to assign charge group codes to atoms of new residue -Regd http://www.mail-archive.com/gmx-users@gromacs.org/msg47706.html <font color=#6f6f6f> 2012/02/08</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Wed, 08 Feb 2012 20:40:23 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47706.html [gmx-users] How to assign charge group codes to atoms of new residue -Regd http://www.mail-archive.com/gmx-users@gromacs.org/msg47705.html <font color=#6f6f6f> 2012/02/08</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22ramesh cheerla%22">ramesh cheerla</a> Wed, 08 Feb 2012 19:05:36 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47705.html Re: [gmx-users] Re: Gromacs analysis tools for Namd output http://www.mail-archive.com/gmx-users@gromacs.org/msg47704.html <font color=#6f6f6f> 2012/02/08</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Ignacio Fernández Galván%22">Ignacio Fernández Galván</a> Wed, 08 Feb 2012 09:35:43 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47704.html Re: [gmx-users] Re: Gromacs analysis tools for Namd output http://www.mail-archive.com/gmx-users@gromacs.org/msg47703.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Francesco Oteri%22">Francesco Oteri</a> Tue, 07 Feb 2012 20:20:00 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47703.html Re: [gmx-users] Re: Gromacs analysis tools for Namd output http://www.mail-archive.com/gmx-users@gromacs.org/msg47702.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Kunze, Micha%22">Kunze, Micha</a> Tue, 07 Feb 2012 19:21:05 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47702.html [gmx-users] Re: Gromacs analysis tools for Namd output http://www.mail-archive.com/gmx-users@gromacs.org/msg47701.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22PAUL NEWMAN%22">PAUL NEWMAN</a> Tue, 07 Feb 2012 18:18:02 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47701.html Re: [gmx-users] rotational diffusion for non-globular proteins http://www.mail-archive.com/gmx-users@gromacs.org/msg47700.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Paymon Pirzadeh%22">Paymon Pirzadeh</a> Tue, 07 Feb 2012 18:02:41 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47700.html Re: [gmx-users] g_rdf http://www.mail-archive.com/gmx-users@gromacs.org/msg47699.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Tue, 07 Feb 2012 15:23:48 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47699.html [gmx-users] g_rdf http://www.mail-archive.com/gmx-users@gromacs.org/msg47698.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Steven Neumann%22">Steven Neumann</a> Tue, 07 Feb 2012 15:16:43 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47698.html Re: [gmx-users] harmonic distance restraints http://www.mail-archive.com/gmx-users@gromacs.org/msg47697.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Tue, 07 Feb 2012 13:34:34 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47697.html Re: [gmx-users] problem with topology generation of ligand http://www.mail-archive.com/gmx-users@gromacs.org/msg47696.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Tue, 07 Feb 2012 13:29:16 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47696.html [gmx-users] harmonic distance restraints http://www.mail-archive.com/gmx-users@gromacs.org/msg47695.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesca vitalini%22">francesca vitalini</a> Tue, 07 Feb 2012 13:29:04 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47695.html [gmx-users] problem with topology generation of ligand http://www.mail-archive.com/gmx-users@gromacs.org/msg47694.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Anushree Tripathi%22">Anushree Tripathi</a> Tue, 07 Feb 2012 11:55:38 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47694.html Re: [gmx-users] overheating problem http://www.mail-archive.com/gmx-users@gromacs.org/msg47693.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22ahmet yıldırım%22">ahmet yıldırım</a> Tue, 07 Feb 2012 08:47:50 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47693.html RE: [gmx-users] Triple bond http://www.mail-archive.com/gmx-users@gromacs.org/msg47692.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Dallas Warren%22">Dallas Warren</a> Tue, 07 Feb 2012 02:22:26 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47692.html RE: [gmx-users] g_rdf and lipid bilayer hydration http://www.mail-archive.com/gmx-users@gromacs.org/msg47691.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Dallas Warren%22">Dallas Warren</a> Tue, 07 Feb 2012 02:18:12 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47691.html [gmx-users] Triple bond http://www.mail-archive.com/gmx-users@gromacs.org/msg47690.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Tanos Franca%22">Tanos Franca</a> Tue, 07 Feb 2012 01:33:43 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47690.html Re: [gmx-users] Using groups in the mdp file http://www.mail-archive.com/gmx-users@gromacs.org/msg47689.html <font color=#6f6f6f> 2012/02/07</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Tue, 07 Feb 2012 00:27:07 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47689.html Re: [gmx-users] a question about membrane simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47688.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Peter C. Lai%22">Peter C. Lai</a> Mon, 06 Feb 2012 23:48:35 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47688.html Re: [gmx-users] Using groups in the mdp file http://www.mail-archive.com/gmx-users@gromacs.org/msg47687.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Ignacio Fernández Galván%22">Ignacio Fernández Galván</a> Mon, 06 Feb 2012 18:34:16 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47687.html Re: [gmx-users] Using groups in the mdp file http://www.mail-archive.com/gmx-users@gromacs.org/msg47686.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Mon, 06 Feb 2012 18:08:26 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47686.html Re: [gmx-users] How to setup a system of a protein attached to a small molecule? http://www.mail-archive.com/gmx-users@gromacs.org/msg47685.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Mon, 06 Feb 2012 17:46:19 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47685.html Re: [gmx-users] Using groups in the mdp file http://www.mail-archive.com/gmx-users@gromacs.org/msg47684.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22francesco oteri%22">francesco oteri</a> Mon, 06 Feb 2012 17:13:58 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47684.html [gmx-users] Using groups in the mdp file http://www.mail-archive.com/gmx-users@gromacs.org/msg47683.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Ignacio Fernández Galván%22">Ignacio Fernández Galván</a> Mon, 06 Feb 2012 16:26:34 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47683.html [gmx-users] a question about membrane simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47682.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Albert%22">Albert</a> Mon, 06 Feb 2012 15:40:02 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47682.html Re: [gmx-users] g_dist http://www.mail-archive.com/gmx-users@gromacs.org/msg47681.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Mon, 06 Feb 2012 14:43:46 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47681.html [gmx-users] g_rdf and lipid bilayer hydration http://www.mail-archive.com/gmx-users@gromacs.org/msg47680.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Ioannis Beis%22">Ioannis Beis</a> Mon, 06 Feb 2012 14:31:43 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47680.html Re: [gmx-users] umbrella-histogram-windows http://www.mail-archive.com/gmx-users@gromacs.org/msg47679.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Mon, 06 Feb 2012 14:11:58 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47679.html Re: [gmx-users] van der waals interaction http://www.mail-archive.com/gmx-users@gromacs.org/msg47678.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Mon, 06 Feb 2012 14:08:17 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47678.html [gmx-users] amber-lipid http://www.mail-archive.com/gmx-users@gromacs.org/msg47677.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22ABEL Stephane 175950%22">ABEL Stephane 175950</a> Mon, 06 Feb 2012 13:18:20 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47677.html Re: [gmx-users] amber-lipid http://www.mail-archive.com/gmx-users@gromacs.org/msg47676.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Steven Neumann%22">Steven Neumann</a> Mon, 06 Feb 2012 13:09:59 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47676.html [gmx-users] a question about membrane simulation http://www.mail-archive.com/gmx-users@gromacs.org/msg47675.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Albert%22">Albert</a> Mon, 06 Feb 2012 13:09:29 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47675.html Re: [gmx-users] Index file http://www.mail-archive.com/gmx-users@gromacs.org/msg47674.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Mon, 06 Feb 2012 13:07:04 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47674.html Re: [gmx-users] amber-lipid http://www.mail-archive.com/gmx-users@gromacs.org/msg47673.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Justin A. Lemkul%22">Justin A. Lemkul</a> Mon, 06 Feb 2012 13:06:51 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47673.html Re: [gmx-users] problem with nvt equilibration http://www.mail-archive.com/gmx-users@gromacs.org/msg47672.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Mark Abraham%22">Mark Abraham</a> Mon, 06 Feb 2012 12:19:19 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47672.html Re: [gmx-users] problem with nvt equilibration http://www.mail-archive.com/gmx-users@gromacs.org/msg47671.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Anushree Tripathi%22">Anushree Tripathi</a> Mon, 06 Feb 2012 12:10:34 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47671.html [gmx-users] amber-lipid http://www.mail-archive.com/gmx-users@gromacs.org/msg47670.html <font color=#6f6f6f> 2012/02/06</font> -- <a href="http://www.mail-archive.com/search?l=gmx-users@gromacs.org&q=from:%22Алексей Раевский%22">Алексей Раевский</a> Mon, 06 Feb 2012 12:04:57 GMT http://www.mail-archive.com/gmx-users@gromacs.org/msg47670.html