Re: [gmx-users] editconf -translate help
Shayla Fitzsimmons wrote: I have a box which contains a slab of carbon (solid) that is centered within the box. However, I want the slab to be at the very right side of the box - I know I must use editconf -translate to do this, however I cannot seem to make it work. The slab is centered has the same height and width (y and z coordinates) of the box, however it is one third of the length (the x coordinate). Graphically, at the moment, it looks like this: _ | xxx | | xxx | |___xxx___| Where 'xx' is my slab (that is how the view comes up when I open the file in rasmol). The dimensions of the box (as listed in the .gro file) are 13.90030 4.02160 5.36640 As I previously said, I want the slab to be on the right side of the box, not the center, however I have tried several different things and it does not seem to want to work for me (however, I am unsure if I am using the proper values for -translate). What X Y Z coordinates should I use for this to translate it? the difference between new and old com. most likely 5 0 0 will do the trick. Thanks! S F ___ 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] superimpose pdbs
Hi! It may be a bit GMX off-topic: I am looking for a command line superimpose application that would be able to get all individual pdb files in folder and generated new pdb versions of them 3D superimposed. Something like what SuperPose ( http://wishart.biology.ualberta.ca/SuperPose/help.html) does, but then locally in my computer. Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ 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] superimpose pdbs
Alan wrote: Hi! It may be a bit GMX off-topic: I am looking for a command line superimpose application that would be able to get all individual pdb files in folder and generated new pdb versions of them 3D superimposed. g_confrms Something like what SuperPose (http://wishart.biology.ualberta.ca/SuperPose/help.html) does, but then locally in my computer. Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ 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] Regarding minimization of POPE:POPG lipid bilayer
I built a POPE:POPG bilayer in 3:1 ratio. Simplify. Start with pure POPE and pure POPG first. When I am minimizing the bilayer, bonds in head groups are breaking in POPE and POPG lipid molecules. Your topologies are incorrect. Start with a simple test system: a single POPE in vaccuum. while creating *.tpr file using the above file for minimization, I am getting fallowing message. calling /lib/cpp... In file included from pg-pe.top:5: dpopg.itp:10:8: warning: multi-line string literals are deprecated Why not take a look at line 10 (or line 8) in dpopg.itp? You are still a long way from simulating a protein in the bilayer. May I recommend that you try a little harder to solve your problems before posting (e.g. by reading the warning messages carefully and seeing what they mean for yourself, or by trying to find a simpler test system to narrow down the problem). In this way you will avoid decreasing your likelihood of receiving answers to the harder problems you may encounter. Good luck. ___ 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] Energy minimization problem with Double precision and mpi
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:gmx-users- [EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. OK, this branch is not yet quite stable, we are still testing things there. It would be good to know whether the release_3_3_patches branch also solves your problem. Installing the release-3-3-patches branch also solves the problem. I only tested it on two nodes ie. -np 2 but I assume it would also work for more. -- 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] Energy minimization problem with Double precision and mpi
Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:gmx-users- [EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. OK, this branch is not yet quite stable, we are still testing things there. It would be good to know whether the release_3_3_patches branch also solves your problem. Installing the release-3-3-patches branch also solves the problem. I only tested it on two nodes ie. -np 2 but I assume it would also work for more. Thanks, that is good to hear. It could be due to parallel minimization, but if it is fixed in CVS I won't investigate it further. -- 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
