[gmx-users] Gromacs version
Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi - 110067. Telephone: 91-11-26717568, 26717585 Facsimile: 91-11-26717586 ** __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ ___ 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] LINCS warning
> Dear all, > I have a query, > 1. Are two trajectories comparable if each one of them > has been run in a different version of gromacs? Eg, > v3.2 and v3.3. Define "comparable". If you mean are they sampling the same thermodynamic ensemble, then the answer is yes if you used the same algorithms. If you mean are they numerically identical, the answer is no. Round-off errors from different order of summation, etc. will cause tiny differences that magnify chaotically. Mark ___ 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] Gromacs version
I think the statistical reserves but the two trajectories are not exactly the same. On 9/9/06, Ragothaman Yennamalli <[EMAIL PROTECTED]> wrote: Dear all,I have a query,1. Are two trajectories comparable if each one of themhas been run in a different version of gromacs? Eg, v3.2 and v3.3.Thanks in advance,Regards,Raghu**Y. M. Ragothaman,Research Scholar,Centre for Computational Biology and Bioinformatics,School of Information Technology, Jawaharlal Nehru University,New Delhi - 110067.Telephone: 91-11-26717568, 26717585Facsimile: 91-11-26717586**__ Yahoo! India Answers: Share what you know. Learn something newhttp://in.answers.yahoo.com/___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 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] problem with dimer simulation !
hi, all user: i performed the dimer simulation, and want to realize the interaction between two peptides. but frequently, i encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back. i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem. for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump ) with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform. any suggestions for me ? thanks sooo much! ___ 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] problem with dimer simulation !
try - cluster, and then as cluster group protein.Kay.On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: hi, all user: i performed the dimer simulation, and want to realize the interaction between two peptides. but frequently, i encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back. i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem. for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump ) with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform. any suggestions for me ? thanks sooo much!___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 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] LINCS warning
hi raghu, in version 3.3 some bugs have been fixed, which you can read on the gromacs website. E.g. the temperature coupling algorithm has been modified, which means that this thermodynamical property is evaluated and assigned differently than in v3.2. This will change your simulations totally, you certainly won't be getting the same trajectories. In any case it's difficult to compare different runs if at the same time you are comparing different softwares. daniela On Sat, 9 Sep 2006 17:15:55 +1000 (EST) "Mark Abraham" <[EMAIL PROTECTED]> wrote: Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Define "comparable". If you mean are they sampling the same thermodynamic ensemble, then the answer is yes if you used the same algorithms. If you mean are they numerically identical, the answer is no. Round-off errors from different order of summation, etc. will cause tiny differences that magnify chaotically. Mark -- Daniela S. Müller Molecular Dynamics (MD) Groningen Biomolecular Sciences and Biotechnology Institute (GBB) MD group website: http://www.rug.nl/gbb/md Address: Daniela S. Mueller Molecular Dynamics group Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands email: [EMAIL PROTECTED] ___ 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] May I use "-b" and "-e" in the cosine con tent calculation of PC?
Hi dear friends, I just made an essential dynamics of 5ns; I calculated the cosine content of PC1 by using g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg it gave: "Cosine content of set 1 with 0.5 periods: 0.749969" the value is rather too high. However, I found that only trajectory between 3300~3890 ps is useful, so I calculated the cosine content during this period using g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890 and it gave: "Cosine content of set 1 with 0.5 periods: 0.297911" I want to know whether the essential dynamics is meaningful? The cosine content of whole 5 ns is relative high, does it mean that the whole trajectory is not meaningful? In another word, is it reasonable to use "-b" and "-e" in the cosine content calculation? Thanks. Stanley Yan 买 房 租 房 二 手 房 请 登 陆 房 老 大 登 陆 房 老 大 ，房 源 遍 天 下 ！房 老 大 - 首 家 专 业 房 源 搜 索 引 擎 ！ ___ 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
