[gmx-users] hessian_matrix_from_ordered_trajectory
Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command trjorder to order the watermolecules in a way so that they are close to the center of mass of the peptide. From this new trajectory I took only the subsystem Peptide+ the first 20 closest water and generated the Hessian. When I look at the input-files,needed to generate the matrix I see that one need only the configuration, a top file and a mdp file. (for grompp). So this would mean, that gromacs would calculate the Potential (the second derivate of the potential) from this configuration and then calculate the hessian matrix. Furthermore I calculated the Hessian at every snapshot of the trajectory. I tested if its work right and calculated the hessian matrix from the same configuration, but only changed 2 watermolecules in their index i. (see the tables below) for example: old configuationnew configuration i coordinates i coord. 12 O xO1 yO1 zO1 12 O xO2 yO2 zO2 12 H xH11 yH11 zH11(change index)12 H xH21 yH21 zH21 12 H xH12 yH12 zH12-- 12 H xH22 y22 zH22 ... ... ... ... 22 O xO2 yO2 zO2 22 O xO1 yO1 zO1 22 H xH21 yH21 zH21 22 H xH11 yH11 zH11 22 H xH22 yH22 zH22 22 H xH12 yH12 zH12 ... ... ... ... In most cases I got the same eigenvalues and eigenvectors but in some cases the results were very different. What could be the reason? Thank you in advance Sang Min ___ 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] hessian_matrix_from_ordered_trajectory
Hi Sang Min, The distance from the center of mass is not a proper identifier for these kinds of calculations. To do this properly, you have to map the water molecules to specific positions around your peptide, and base your identifiers on that. E.g. if you have: H2O-peptide--OH2 and H2O--peptide-OH2, your identifiers, based on the shortest distance, interchange, but so does the position w.r.t. the peptide! This is largely unrelated to the center of mass (and more so the further you go from it). There's no sense in trying to do NMA like that. If you get it right, it'll make a very nice study though. Best, Tsjerk On 4/5/07, Sang-Min Park [EMAIL PROTECTED] wrote: Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command trjorder to order the watermolecules in a way so that they are close to the center of mass of the peptide. From this new trajectory I took only the subsystem Peptide+ the first 20 closest water and generated the Hessian. When I look at the input-files,needed to generate the matrix I see that one need only the configuration, a top file and a mdp file. (for grompp). So this would mean, that gromacs would calculate the Potential (the second derivate of the potential) from this configuration and then calculate the hessian matrix. Furthermore I calculated the Hessian at every snapshot of the trajectory. I tested if its work right and calculated the hessian matrix from the same configuration, but only changed 2 watermolecules in their index i. (see the tables below) for example: old configuationnew configuration i coordinates i coord. 12 O xO1 yO1 zO1 12 O xO2 yO2 zO2 12 H xH11 yH11 zH11(change index)12 H xH21 yH21 zH21 12 H xH12 yH12 zH12-- 12 H xH22 y22 zH22 ... ... ... ... 22 O xO2 yO2 zO2 22 O xO1 yO1 zO1 22 H xH21 yH21 zH21 22 H xH11 yH11 zH11 22 H xH22 yH22 zH22 22 H xH12 yH12 zH12 ... ... ... ... In most cases I got the same eigenvalues and eigenvectors but in some cases the results were very different. What could be the reason? Thank you in advance Sang Min ___ 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 -- 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hessian_matrix_from_ordered_trajectory
On Thu, 5 Apr 2007 18:53:58 +0200 Sang-Min Park [EMAIL PROTECTED] wrote: Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command trjorder to order the watermolecules in a way so that they are close to the center of mass of the peptide. From this new trajectory I took only the subsystem Peptide+ the first 20 closest water and generated the Hessian. When I look at the input-files,needed to generate the matrix I see that one need only the configuration, a top file and a mdp file. (for grompp). So this would mean, that gromacs would calculate the Potential (the second derivate of the potential) from this configuration and then calculate the hessian matrix. Furthermore I calculated the Hessian at every snapshot of the trajectory. I tested if its work right and calculated the hessian matrix from the same configuration, but only changed 2 watermolecules in their index i. (see the tables below) for example: old configuation new configuration i coordinates i coord. 12 O xO1 yO1 zO1 12 O xO2 yO2 zO2 12 H xH11 yH11 zH11(change index)12 H xH21 yH21 zH21 12 H xH12 yH12 zH12-- 12 H xH22 y22 zH22 ... ... ... ... 22 O xO2 yO2 zO2 22 O xO1 yO1 zO1 22 H xH21 yH21 zH21 22 H xH11 yH11 zH11 22 H xH22 yH22 zH22 22 H xH12 yH12 zH12 ... ... ... ... In most cases I got the same eigenvalues and eigenvectors but in some cases the results were very different. What could be the reason? Thank you in advance Sang Min ___ 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 I'm not sure if I understand you correctly : You generated a configuration file of the 20 nearest water molecules. That means that the index and identity of the 20 waters can differ in each snapshot, however in the top file 20 is 20 and names neither numbers don't matter. So the actual identity should not play a role in for the production of tpr. No you switch the order of lets say: water molecule 19 with 20. When you do this you find different eigenvalues of the hessian in some casescorrect ? The dimension of the hessian is Nx3,Nx3, in which you have i=1,2Nx3 rows and collums. Each element i has the same order as in the gro file (1,2N). So if you switch a line in the gro the hessian is different too. Although the hessian will allways be build up from the same set of numbers...it will simply not be the same matrix (permutations). So actually I don't really think this way is a good way to study the time evolution of the hessian. Better just take the protein, peptide or wathever without the water. Did you check if the trace of the hessian (sum of all eigen values) is more close to constant ? Anyway, Good luck. greetings Jelger ___ 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
