Re: [gmx-users] g_rotacf, order parameter S2 problem
Dechang Li wrote: Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is one of my results: Your simulation may be too short. You should look at the average value of the tail over a long time. Check J. Chem. Theor. Comp. 2 (2006) 1228 @title Rotational Correlation Function @xaxis label Time (ps) @yaxis label C(t) @TYPE xy ... 119944.000-0.16902 119946.000-0.16845 119948.000-0.16812 119950.000-0.16845 119952.000-0.16834 119954.000-0.16825 119956.000-0.16875 119958.000-0.16823 119960.000-0.16850 119962.000-0.16885 119964.000-0.16892 119966.000-0.16924 119968.000-0.16885 119970.000-0.16928 119972.000-0.16889 119974.000-0.16901 119976.000-0.16866 119978.000-0.16901 119980.000-0.16895 119982.000-0.16953 119984.000-0.16932 119986.000-0.16961 119988.000-0.16947 119990.000-0.16890 119992.000-0.16952 119994.000-0.16986 119996.000-0.16970 119998.000-0.16941 12.000-0.16908 The command I used is : g_rotacf -s Order.tpr -f Order.trr -d -n index.ndx -P 2 -nice 0 . Actually, when I used the option -P 1, the negative results appear similarly. Before I calculated the S2 parameter, I removed the rotation and translation movement of the molecule using the tool trjconv. Is that the negative results reasonable? Best regards, 2009-1-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about complexing protein and ligand
Shirin Awasthi wrote: I want to know if there is any way in gromacs where i can complex a docked ligand mol2 file with the parent receptor protein. i have the mol2 file file consisting of the translated coordinates for the ligand. my desired output is one pdb file for the docked ligand-receptor complex. You sound like you are looking for a docking program, not a molecular dynamics suite. Mark ___ 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
Re: [gmx-users] eigenvalues
So just to make sure i got this correct, when looking at the cosine content of the principal components i should look at the whole trajectory? Do i need to include the initial relaxation in the first few ns of the production simulation? If there is a high cosine content for the whole trajectory is there anything else to be done (if i want to look at the low frequency motions of the trajectory) except for simulate for longer (i have a very large system so not the favoured option!)? As you say it seems that lots of people use PCA on short trajectories, even of large systems, which to me is confusing Thanks for any insights you can give Tom --On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sanjay, Imagine yourself zig-zagging along a line from one place to another. If you look at you're motion (and the variance), you'll find that if you only look at blocks most of it is explained by the zig-zag and nicely periodic (no cosine content as in Berk Hess' paper). Good, you think. But if you look at the whole travel, the most important contribution is the going from one place to another, and if you look at you're displacement over time with respect to the mean, that will give you half a cosine. The fact that results in a block do not fit a cosine does not take away the fact that you're still in the process of relaxation. I know it's not what you want to hear, but I've seen it happen to a complex of 600 residues, where relaxation took more than 30 ns. I also know that people often do PCA on short time trajectories, but it's not the proper thing to do. Cheers, Tsjerk On Sat, Jan 10, 2009 at 7:34 AM, sanja...@iitb.ac.in wrote: Hi Tsjerk, thanks actually my protein is quite larg (509 aa).i had divided my trajectory in different part and according to your suggestion i calculated cosine-content for all, and find that trajectory from 5to15 ns and 18to25ns having cosine value very less about 0.03 in both cases(with and without ligands), while other combination showing higher values (0.6).so i think my system is Ist converges around 5ns and maintaining it up to 15 ns after that it may be few conformational fluctuation occurring and finally it get stabilized from 18to15ns.may that part 15to18ns trajectory is transition period between to conformational fluctuation. i have also calculated temp. and pressure during whole simulation and i find that it is exact Gaussian between 5to25ns.so my confusion is whether i take my trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25, but 5to25 showing value of cosine 0.6. ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ 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
Re: [gmx-users] eigenvalues
Hey Tom, Tough. It seems like two oppositish things: don't use too short parts to comfort you with the idea that there's no relaxation taking place, but also discard the first part of the simulation to make sure you cut on the equilibration. If you try to bring these two in line with each otherr it sums up to extracting the last, but long enough, chunk of the trajectory that doesn't give you a high cosine content. The fact that a lot of people use PCA on (too) short trajectories reflects that many people don't really understand what it is, and can and can not do. It's one of these tthings that will always give you answers, but requires care to yield sensible answers. It's easy to imagine that many collective motions reported in literature as reflecting functional mechanics are actually just relaxation from the starting structure. Then again, e.g. crystal packing forces are most likely to effect the largest modes, which may well be linked to functional mechanics, but that should then be stated with the analysis as an explicit assumption, together with some sort of justification. Hope it sheds some light. Cheers, Tsjerk On Sun, Jan 11, 2009 at 7:51 PM, TJ Piggot t.pig...@bristol.ac.uk wrote: So just to make sure i got this correct, when looking at the cosine content of the principal components i should look at the whole trajectory? Do i need to include the initial relaxation in the first few ns of the production simulation? If there is a high cosine content for the whole trajectory is there anything else to be done (if i want to look at the low frequency motions of the trajectory) except for simulate for longer (i have a very large system so not the favoured option!)? As you say it seems that lots of people use PCA on short trajectories, even of large systems, which to me is confusing Thanks for any insights you can give Tom --On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sanjay, Imagine yourself zig-zagging along a line from one place to another. If you look at you're motion (and the variance), you'll find that if you only look at blocks most of it is explained by the zig-zag and nicely periodic (no cosine content as in Berk Hess' paper). Good, you think. But if you look at the whole travel, the most important contribution is the going from one place to another, and if you look at you're displacement over time with respect to the mean, that will give you half a cosine. The fact that results in a block do not fit a cosine does not take away the fact that you're still in the process of relaxation. I know it's not what you want to hear, but I've seen it happen to a complex of 600 residues, where relaxation took more than 30 ns. I also know that people often do PCA on short time trajectories, but it's not the proper thing to do. Cheers, Tsjerk On Sat, Jan 10, 2009 at 7:34 AM, sanja...@iitb.ac.in wrote: Hi Tsjerk, thanks actually my protein is quite larg (509 aa).i had divided my trajectory in different part and according to your suggestion i calculated cosine-content for all, and find that trajectory from 5to15 ns and 18to25ns having cosine value very less about 0.03 in both cases(with and without ligands), while other combination showing higher values (0.6).so i think my system is Ist converges around 5ns and maintaining it up to 15 ns after that it may be few conformational fluctuation occurring and finally it get stabilized from 18to15ns.may that part 15to18ns trajectory is transition period between to conformational fluctuation. i have also calculated temp. and pressure during whole simulation and i find that it is exact Gaussian between 5to25ns.so my confusion is whether i take my trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25, but 5to25 showing value of cosine 0.6. ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK.
