[gmx-users] g_sorient with -v23 option
Hi, all, I try to use g_sorient program to analyze SPC water molecules orientation around atomic ion. As I understand two molecule vectors are analyzed. For theta_1 calculation the dipole moment direction is used. Other two orthogonal vectors may be analyzed through theta_2 depending on -v23 option. But I see that this option have an influence also on theta_1 in sori.xvg, sord.xvg and scum.xvg output files! 1. What is the reason? 2. When is the correct theta_1 calculated? -- Regards, Dmitri mailto:ddu...@ngs.ru-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_sorient
Dear all when i try to run g_sorient with g_sorient -f prod_full.xtc -s prod.tpr -o ANALYSIS/sorie nt/sori.xvg -no ANALYSIS/sorient/snor.xvg -ro ANALYSIS/sorient/sord.xvg I am getting a segmentation fault what would be the problem could anyone help in in this regard E R Azhagiya singam -- gmx-users mailing listgmx-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] g_sorient -ro output
Hi, all! I have a question about interpreting the output from a GROMACS tool, g_sorient. I'm analising the solvent orientation around some specific atoms of my molecules, using GROMACS 3.3.3. I have read the mailing lists, but I could not find anything specific about it (although the following discussions have helped me a lot, regarding which output - o, no, ro, co - could better answer my questions): http://www.gromacs.org/pipermail/gmx-users/2002-April/001374.html http://www.gromacs.org/pipermail/gmx-users/2002-April/001375.html http://www.gromacs.org/pipermail/gmx-users/2002-April/001376.html http://www.gromacs.org/pipermail/gmx-users/2002-April/001377.html In addition, I could only find few references with such analysis, but I could not understand its meaning from them. Concerning the -ro output, I have retrieved two different results, depending on the atom I'm analising: negative or positive values of cos(theta) distribution along hydrogen-bonding distances (2.5 to 3.5 angstrons). As far as I could understand, g_sorient outputs: --- (1) a negative value on the distribution around hydrogen bond distances, when water molecules are predominantly performing hydrogen bonds with the atom, as follows: ATOMH--O \ H (2) a positive value on the distribution around hydrogen bond distances, when water molecules have their hydrogens pointing predominantly away from the atom, as follows: H / ATOM O \ H --- Is my interpretation right? Thanks in advance, Laércio Pol-Fachin Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sorient segmenation fault
Hi All, I have been getting segmenation fault with current(3.3.1) version of g_sorient. Dose anybody know why? With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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] g_sorient segmenation fault
Naser, Md Abu wrote: Hi All, I have been getting segmenation fault with current(3.3.1) version of g_sorient. Dose anybody know why? please submit a bugzilla. With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___ 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 van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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
RE: [gmx-users] g_sorient. Again.
From: Eudes Fileti [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] g_sorient. Again. Date: Tue, 30 Jan 2007 22:57:45 -0200 Dear Berk, Thank you for the reply. Actually my problem is not related to the analysis of bonds but of angles. Specifically, I am interested in the distribution of the angle I between the C=C bond of etanol with a plan of my solute molecule. It also would be interesting to analyze as this angle varies with the distance, since I believe that solute modifies significantly the local structure of the solvent. Could you suggest me a procedure or tool? My suggestion is exactly for the angles. If the first C is atom 1 and the second atom 2, then an index group of 1 2 2 results in the dipole in g_sorient being the C=C vector. You can then analyze bond orientations by looking at the dipole angles. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_sorient to ethanol
Good ideia Dr Hess! Only more thing. I would have to rerun the simulation to make the C atoms of ethanol 1 and 2 (since my C atoms have index 1 and 5)? Or there is another more practical way of change the index of atoms? eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_sorient to ethanol
From: Eudes Fileti [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] g_sorient to ethanol Date: Wed, 31 Jan 2007 10:24:59 -0200 Good ideia Dr Hess! Only more thing. I would have to rerun the simulation to make the C atoms of ethanol 1 and 2 (since my C atoms have index 1 and 5)? Or there is another more practical way of change the index of atoms? Then you make an index group as such: 1 5 5 10 14 14 etc. (if your ethanol has 9 atoms) Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_sorient to ethanol
From: Eudes Fileti [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] g_sorient to ethanol Date: Wed, 31 Jan 2007 10:24:59 -0200 Good ideia Dr Hess! Only more thing. I would have to rerun the simulation to make the C atoms of ethanol 1 and 2 (since my C atoms have index 1 and 5)? Or there is another more practical way of change the index of atoms? Then you make an index group as such: 1 5 5 10 14 14 etc. (if your ethanol has 9 atoms) Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_sorient. Only for water?
Dear GMX users The tool g_sorient is applicable only when the solvent is the water? I have attemped to apply it for the case of solvation in ethanol and I am not obtaining an appropriate vector for the calculation of the angle. In fact, it woul be very nice if I can make the C=C bond of ethanol like a vector. Some suggestion? eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_sorient. Only for water?
From: Eudes Fileti [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] g_sorient. Only for water? Date: Tue, 30 Jan 2007 14:43:23 -0200 Dear GMX users The tool g_sorient is applicable only when the solvent is the water? I have attemped to apply it for the case of solvation in ethanol and I am not obtaining an appropriate vector for the calculation of the angle. In fact, it woul be very nice if I can make the C=C bond of ethanol like a vector. Some suggestion? eef I had written it for a project on water. It would indeed be useful to generalize it. But I guess that for a analysis of bonds one could use g_sorient if one makes an index group with triplets such as: 1 2 2 Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_sorient. Again.
Dear Berk, Thank you for the reply. Actually my problem is not related to the analysis of bonds but of angles. Specifically, I am interested in the distribution of the angle I between the C=C bond of etanol with a plan of my solute molecule. It also would be interesting to analyze as this angle varies with the distance, since I believe that solute modifies significantly the local structure of the solvent. Could you suggest me a procedure or tool? Bests eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 CEP 09210-170 skype: eefileti ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
