Re: [gmx-users] Problem with trjconv and centering bilayer.
Ioannis Beis wrote: Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the membrane lies on the lowest part of the box and the lower part of the membrane on the highest part of the box, with the water in the middle. There should not be anything wrong with drifting along the z-axis, since the initial structure was at the very bottom of the box, so even a small drift downwards -due to the pbc- would place the lower part of the membrane on the top of the box. I tried issuing: trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o my_trajectory_no_jump.xtc -pbc nojump with 0 (for system) and subsequently trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol with 1 (other) for centering and 0 (system) for output. I used this kind of commands some time ago and they worked fine. Now strangely the bilayer remains around the position that I described in the beginning. Is it possible that the program treats the bilayer separated as it looks in vmd and considers the geometrical center in the middle of the water instead of the middle of the bilayer? That's exactly what it does. I tried the -trans flag to translate the bilayer along z-axis near the center and repeated the steps, but the new trajectory wasn't even visible in vmd. In addition, the .gro files generated by trjconv are apparently trajectory files instead of structure files. I don't feel confident about using editconf for operations like translation of a single initial structure, because as far as I understand editconf is a tool meant mostly for setting up systems; thus I was sceptical about messing a structure with editconf that I would later on use together with an .xtc file as input for trjconv. However, trjconv doesn't seem to generate structure output files. I don't understand the meaning of a .gro file as trajectory file since there are already at least 3 file formats for trajectories. Generally speaking, a trajectory is just a series of coordinates, so you can output it into a number of formats, including .gro and .pdb, among others. You get a chain of coordinate files that may (or may not) end up being useful in some applications. So how can I bring my bilayer's trajectory in the center of the unit cell for reliable thickness calculation without drifts? Is it possible at the same time to have clear visualization without disturbances? trjconv with -pbc mol still gives rise to lines in the visualization, apparently as a result of atom jumps. Sadly trajectory files cannot be inspected and visualization is quite handy for certain types of feedback in various data analysis-related tasks, so it would be nice if the trajectories used for analysis also look proper in vmd. I can think of two approaches, the first of which I have used so it should work ;) 1. Provide a custom index group specifying only a single lipid atom from the end of a hydrocarbon chain and center on it. Therefore, its geometric center has to be the center of the box, and it should bring the rest of the membrane to the (visual) center of the unit cell. 2. Calculate the distance with the trajectory you have now, and subtract it from the z-length (assuming the membrane plane is x-y) of the box (stored in the .edr file). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Problem with trjconv and centering bilayer.
Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the membrane lies on the lowest part of the box and the lower part of the membrane on the highest part of the box, with the water in the middle. There should not be anything wrong with drifting along the z-axis, since the initial structure was at the very bottom of the box, so even a small drift downwards -due to the pbc- would place the lower part of the membrane on the top of the box. I tried issuing: trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o my_trajectory_no_jump.xtc -pbc nojump with 0 (for system) and subsequently trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol with 1 (other) for centering and 0 (system) for output. I used this kind of commands some time ago and they worked fine. Now strangely the bilayer remains around the position that I described in the beginning. Is it possible that the program treats the bilayer separated as it looks in vmd and considers the geometrical center in the middle of the water instead of the middle of the bilayer? I tried the -trans flag to translate the bilayer along z-axis near the center and repeated the steps, but the new trajectory wasn't even visible in vmd. In addition, the .gro files generated by trjconv are apparently trajectory files instead of structure files. I don't feel confident about using editconf for operations like translation of a single initial structure, because as far as I understand editconf is a tool meant mostly for setting up systems; thus I was sceptical about messing a structure with editconf that I would later on use together with an .xtc file as input for trjconv. However, trjconv doesn't seem to generate structure output files. I don't understand the meaning of a .gro file as trajectory file since there are already at least 3 file formats for trajectories. So how can I bring my bilayer's trajectory in the center of the unit cell for reliable thickness calculation without drifts? Is it possible at the same time to have clear visualization without disturbances? trjconv with -pbc mol still gives rise to lines in the visualization, apparently as a result of atom jumps. Sadly trajectory files cannot be inspected and visualization is quite handy for certain types of feedback in various data analysis-related tasks, so it would be nice if the trajectories used for analysis also look proper in vmd. Thank you in advance. Best regards, Ioannis -- 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] problem with trjconv -pbc cluster
I wrote my own program to do this and so I never tried that one. We did find that clustering based on a dingle atom in the chain was a very good idea. So take your distal carbon in the surfactant and make in index group of it and cluster it (with a larger cutoff) with g_clustsize. Obviously if there is a problem with g_clustsize then you should also file a bugzilla. If you're going to continue with this thread about g_clustsize, then please pick an appropriate subject line so that others can search it usefully later. Chris. -- original message -- Hi Chris, Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. As I mentioned, if I visualize the trajectory in VMD, I see that starting from a random dispersed state of 50 molecules of surfactant, it aggregates gradually and at a long time, two distinct miceller aggregates are formed.But, If I try to quantify the cluster-size distribution using g_clustsize utilty, it gives me bizarre results: the maxclust.xvg for the final time frame shows that I have 1 single cluster containing all the 50 molecules. But, Vmd shows 2 distinct aggregate. Here is the command line I used: g_clustsize -f traj.xtc -s topol -mol -cut 0.50 I used -mol option so that I get the cluster size distribution in terms of the molecules.Here, executing the commands gives me maxclust.xvg which has maximum size of clusters( in terms of molecule number) as a function of time frame. It shows at the end, maxclustersize is 50 and it has all the particles in it( as obtained from maxclust.ndx)Besides, at any other time, the maximum size of particles predicted by g_clustsize does not match with what VMD shows. I also tried post-processing the trajectory using trjconv with -pbc whole or with -pbc nojump . But, g_clustsize always returns same result:maxcluster contains all the particles.Then I tried playing with -cut option : I started with default value of 0.35, here the result is worse: it shows maxclust = 1 i.e all the particles are monomeric . But any value beyond 0.35 gives me maxclust = 50. I tried to cross-check whether visualization is misrepresented or not: for this I tried to calculate all the distances among the com of the surfectants using g_dist tool and tried to manually cluster the surfectants and I found that here I can easily come up with two separate cluster based on the distances. So, I think that the problem lies in g_clustsize not in visualization, as -pbc whole or -pbc nojump does not change the result.So, do you have any suggestions ? Any help in pointing out where I am doing wrong will be helpful.Jagannath --- On Wed, 7/7/10, chris.neale at utoronto.ca utoronto.ca> wrote: From: chris.neale at utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users at gromacs.org Date: Wednesday, 7 July, 2010, 9:27 PM -- 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
Re: [gmx-users] problem with trjconv -pbc cluster
Hi Chris, Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. As I mentioned, if I visualize the trajectory in VMD, I see that starting from a random dispersed state of 50 molecules of surfactant, it aggregates gradually and at a long time, two distinct miceller aggregates are formed.But, If I try to quantify the cluster-size distribution using g_clustsize utilty, it gives me bizarre results: the maxclust.xvg for the final time frame shows that I have 1 single cluster containing all the 50 molecules. But, Vmd shows 2 distinct aggregate. Here is the command line I used: g_clustsize -f traj.xtc -s topol -mol -cut 0.50 I used -mol option so that I get the cluster size distribution in terms of the molecules.Here, executing the commands gives me maxclust.xvg which has maximum size of clusters( in terms of molecule number) as a function of time frame. It shows at the end, maxclustersize is 50 and it has all the particles in it( as obtained from maxclust.ndx)Besides, at any other time, the maximum size of particles predicted by g_clustsize does not match with what VMD shows. I also tried post-processing the trajectory using trjconv with -pbc whole or with -pbc nojump . But, g_clustsize always returns same result:maxcluster contains all the particles.Then I tried playing with -cut option : I started with default value of 0.35, here the result is worse: it shows maxclust = 1 i.e all the particles are monomeric . But any value beyond 0.35 gives me maxclust = 50. I tried to cross-check whether visualization is misrepresented or not: for this I tried to calculate all the distances among the com of the surfectants using g_dist tool and tried to manually cluster the surfectants and I found that here I can easily come up with two separate cluster based on the distances. So, I think that the problem lies in g_clustsize not in visualization, as -pbc whole or -pbc nojump does not change the result.So, do you have any suggestions ? Any help in pointing out where I am doing wrong will be helpful.Jagannath --- On Wed, 7/7/10, chris.ne...@utoronto.ca wrote: From: chris.ne...@utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org Date: Wednesday, 7 July, 2010, 9:27 PM PS: you realize that trjconv -pbc cluster is never going to work unless you actually have a cluster, right? So you can't start this procedure near your initial dispersed state. You need to start at some time T where you actually do have a cluster. Then you can try -dump T, -dump (T+X), -dump (T+X*2), etc. Then you can follow the ides expressed below like running backwards with -pbc nojup to get the initial state. Chris. --original message -- Dear Jagannath: There is, as far as I know, no way to fix this. Here's what you should do. 1. Let the space between your timesteps be X ps. 2. Use trjconv -pbc cluster -dump X -o out.gro 2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro 2c. if that doesn't work, try trjconv -pbc cluster -dump (X*3) -o out.gro ... (Note use real numbers for args to -dump). Once you have a frame that works, you can run part 2 and 3 of that wiki page by making a tpr based on the gro that worked -- and I think that you'll need to run your trjconv -pbc mol starting from the frame where clustering worked (e.g. -b X). Note that this second requirement means that you may need to reverse the frames from your .xtc file so that you can run in reverse time from a complete micelle through to disassembly with -pbc nojump -- a for loop around trjconv will work but inefficiently, you might be able to use -demux smartly here (I'm not sure). But then since you have 2 micelles you will need a starting box in which they are both whole getting trickier. You should be aware that the trjconv -pbc cluster is not the only way to do part 1 from that wiki page. You could use trjconv -trans X Y Z and then make a new .tpr and then run trjconv -pbc nojump and it would work if only you knew which X Y Z to use (although trial and error may help you here eventually). Sorry this is confusing, but this is a difficult thing to do and you should expect to struggle with it for some time, so another questino to ask yourself is "do I really need to do this?" If its just for making a movie then you can use pbctools in vmd for that. Chris. -- original message -- Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.e use
[gmx-users] problem with trjconv -pbc cluster
PS: you realize that trjconv -pbc cluster is never going to work unless you actually have a cluster, right? So you can't start this procedure near your initial dispersed state. You need to start at some time T where you actually do have a cluster. Then you can try -dump T, -dump (T+X), -dump (T+X*2), etc. Then you can follow the ides expressed below like running backwards with -pbc nojup to get the initial state. Chris. --original message -- Dear Jagannath: There is, as far as I know, no way to fix this. Here's what you should do. 1. Let the space between your timesteps be X ps. 2. Use trjconv -pbc cluster -dump X -o out.gro 2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro 2c. if that doesn't work, try trjconv -pbc cluster -dump (X*3) -o out.gro ... (Note use real numbers for args to -dump). Once you have a frame that works, you can run part 2 and 3 of that wiki page by making a tpr based on the gro that worked -- and I think that you'll need to run your trjconv -pbc mol starting from the frame where clustering worked (e.g. -b X). Note that this second requirement means that you may need to reverse the frames from your .xtc file so that you can run in reverse time from a complete micelle through to disassembly with -pbc nojump -- a for loop around trjconv will work but inefficiently, you might be able to use -demux smartly here (I'm not sure). But then since you have 2 micelles you will need a starting box in which they are both whole getting trickier. You should be aware that the trjconv -pbc cluster is not the only way to do part 1 from that wiki page. You could use trjconv -trans X Y Z and then make a new .tpr and then run trjconv -pbc nojump and it would work if only you knew which X Y Z to use (although trial and error may help you here eventually). Sorry this is confusing, but this is a difficult thing to do and you should expect to struggle with it for some time, so another questino to ask yourself is "do I really need to do this?" If its just for making a movie then you can use pbctools in vmd for that. Chris. -- original message -- Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.euse trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.use grompp to make a new tpr file based on the frame that was output from the step above.use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro -o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence. I am using gromacs 4.0.7 Any help will be appreciated. Jagannath -- 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] problem with trjconv -pbc cluster
Dear Jagannath: There is, as far as I know, no way to fix this. Here's what you should do. 1. Let the space between your timesteps be X ps. 2. Use trjconv -pbc cluster -dump X -o out.gro 2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro 2c. if that doesn't work, try trjconv -pbc cluster -dump (X*3) -o out.gro ... (Note use real numbers for args to -dump). Once you have a frame that works, you can run part 2 and 3 of that wiki page by making a tpr based on the gro that worked -- and I think that you'll need to run your trjconv -pbc mol starting from the frame where clustering worked (e.g. -b X). Note that this second requirement means that you may need to reverse the frames from your .xtc file so that you can run in reverse time from a complete micelle through to disassembly with -pbc nojump -- a for loop around trjconv will work but inefficiently, you might be able to use -demux smartly here (I'm not sure). But then since you have 2 micelles you will need a starting box in which they are both whole getting trickier. You should be aware that the trjconv -pbc cluster is not the only way to do part 1 from that wiki page. You could use trjconv -trans X Y Z and then make a new .tpr and then run trjconv -pbc nojump and it would work if only you knew which X Y Z to use (although trial and error may help you here eventually). Sorry this is confusing, but this is a difficult thing to do and you should expect to struggle with it for some time, so another questino to ask yourself is "do I really need to do this?" If its just for making a movie then you can use pbctools in vmd for that. Chris. -- original message -- Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.euse trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.use grompp to make a new tpr file based on the frame that was output from the step above.use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro -o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence. I am using gromacs 4.0.7 Any help will be appreciated. Jagannath -- 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
Re: [gmx-users] problem with trjconv -pbc cluster
Thanks for the reply. I used following command to extract first frame that has all the surfectants ( as suggested by first step for characterizing micelle clustering). trjconv -f a.xtc -o a_cluster.gro -dump 0 -pbc cluster Here is the output I got:COM: 0.000 0.000 19.999 iter = 19526 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19527 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19528 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19529 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19530 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19531 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19532 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19533 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19534 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19535 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19536 Isq = 12671033.000COM: 0.000 0.000 0.000 iter = 19537 Isq = 12628369.000COM: 0.000 0.000 19.999 iter = 19538 Isq = 12671033.000 looks like lsq is only fluctuating between two numbers and the program is in an infinte loop. Jagannath --- On Wed, 7/7/10, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] problem with trjconv -pbc cluster To: "Discussion list for GROMACS users" Date: Wednesday, 7 July, 2010, 12:20 PM - Original Message - From: jagannath mondal Date: Wednesday, July 7, 2010 16:36 Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org > Hi, I had a system of surfectants which are started with an initial > configuration where all of them are well dispersed. Visual study of > trajectory shows they start aggregating and finally form two discrete > micelles. > To quantify this micelle clusterization, I tried to use the > suggestions present in the gromacs documentations:> > http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering> > i.e > > use trjconv -pbc cluster to obtain a single frame that has all of > the lipids in the unit cell. This must be the first frame of your > trajectory. A similar frame from some previous timepoint will not work.> > use grompp to make a new tpr file based on the frame that was output from the > step above.> use trjconv -pbc nojump to produce the desired trajectory using > the newly produced tpr file.> trjconv -f a.xtc -o a_cluster.gro -e 0.001 > -pbc cluster> grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr> trjconv -f > a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump > But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is > going through an infinite loop and is not stopping for convergence. So what command did you give, what output did you get, and does the command make sense with respect to your trajectory contents? Mark > > I am using gromacs 4.0.7> > Any help will be appreciated.> > Jagannath> > -- > gmx-users mailing list gmx-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 -Inline Attachment Follows- -- gmx-users mailing list gmx-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 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
Re: [gmx-users] problem with trjconv -pbc cluster
- Original Message - From: jagannath mondal Date: Wednesday, July 7, 2010 16:36 Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org --- | > Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. > To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations:> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering> > i.e > - > use trjconv -pbc cluster to obtain a single frame that has all > of the lipids in the unit cell. This must be the first frame of your > trajectory. A similar frame from some previous timepoint will not work. - > use grompp to make a new tpr file based on the frame that was output from the step above. - > use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file. - > trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster - > grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr - > trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump > But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is > going through an infinite loop and is not stopping for convergence. So what command did you give, what output did you get, and does the command make sense with respect to your trajectory contents? Mark > > I am using gromacs 4.0.7> > Any help will be appreciated.> > Jagannath | --- > > -- > 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 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] problem with trjconv -pbc cluster
Hi, I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present in the gromacs documentations: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering i.euse trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.use grompp to make a new tpr file based on the frame that was output from the step above.use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro -o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump But, The first step i.e. trjconv -pbc cluster does not work. Looks like it is going through an infinite loop and is not stopping for convergence. I am using gromacs 4.0.7 Any help will be appreciated. Jagannath -- 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
Re: [gmx-users] problem with trjconv
nitu sharma wrote: Dear all I am on the final step of MD simulation of membrane protein . the final mdrun has successfully completed after that I have filtered the water from the system .next step is to convert it in final pdb to view it in pymol for this I am using "trjconv" in this step I have to select a group from this option- Group 0 ( System) has 419010 elements Group 1 ( Protein) has 9902 elements Group 2 ( Protein-H) has 7778 elements Group 3 ( C-alpha) has 1000 elements Group 4 (Backbone) has 3000 elements Group 5 ( MainChain) has 4000 elements Group 6 (MainChain+Cb) has 4922 elements Group 7 ( MainChain+H) has 4961 elements Group 8 ( SideChain) has 4941 elements Group 9 ( SideChain-H) has 3778 elements Group10 ( Prot-Masses) has 9902 elements Group11 ( Non-Protein) has 409108 elements Group12 (DMPC) has 5520 elements Group13 ( SOL) has 403578 elements Group14 ( NA+) has10 elements Group15 ( Other) has 409108 elements Select a group: for protein with lipid bilayer which group is suitable can anyone suggest me? It seems to me that you haven't actually "filtered water", but that you may wish to create a suitable index group. See http://oldwiki.gromacs.org/index.php/Index_File Mark Becoz a/c to my opinion in group 0 there may be water also but I want to remove water . so please if anyone have idea about this please suggest me . thanks a lot. Nitu Sharma. ___ 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 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] problem with trjconv
Dear all I am on the final step of MD simulation of membrane protein . the final mdrun has successfully completed after that I have filtered the water from the system .next step is to convert it in final pdb to view it in pymol for this I am using "trjconv" in this step I have to select a group from this option- Group 0 ( System) has 419010 elements Group 1 ( Protein) has 9902 elements Group 2 ( Protein-H) has 7778 elements Group 3 ( C-alpha) has 1000 elements Group 4 (Backbone) has 3000 elements Group 5 ( MainChain) has 4000 elements Group 6 (MainChain+Cb) has 4922 elements Group 7 ( MainChain+H) has 4961 elements Group 8 ( SideChain) has 4941 elements Group 9 ( SideChain-H) has 3778 elements Group10 ( Prot-Masses) has 9902 elements Group11 ( Non-Protein) has 409108 elements Group12 (DMPC) has 5520 elements Group13 ( SOL) has 403578 elements Group14 ( NA+) has10 elements Group15 ( Other) has 409108 elements Select a group: for protein with lipid bilayer which group is suitable can anyone suggest me? Becoz a/c to my opinion in group 0 there may be water also but I want to remove water . so please if anyone have idea about this please suggest me . thanks a lot. Nitu Sharma. ___ 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
Re: [gmx-users] problem with trjconv
> Hi all, > I am trying to use *trjconv command for -pbc but POPC molecules are > breaking > when visualize in VMD. The commands used are > grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr > trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster > or > whole > Thi trj_out.gro contain broken POPC molecules GROMACS doesn't ever write molecules that are broken across periodic boundaries. Thus either you've introduced a visual artefact with your use of VMD, or your EM produced a broken molecule through using a broken physical model. You should examine the nature of "broken", and/or try using ngmx to confirm what is really going on. Your grompp-trjconv sequence is not necessary for massaging the PBC behaviour of your EM output. trjconv will accept a .gro file for the -s flag, which you will see is indicated in the section of the output of "trjconv -h" that deals with the -s flag. This is quite general GROMACS behaviour. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with trjconv
Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi all, > I am trying to use *trjconv command for -pbc but POPC molecules are breaking > when visualize in VMD. The commands used are > grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr > trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or > whole Your scheme will not work because the structure in the .tpr file is the same as in your em_out.gro, which you claim to be broken. I'm assuming em_out.gro refers to your structure following energy-minimization? And if so, I'm wondering what you've done that's left a broken molecule following EM. Is your em_out.gro whole? -Justin > Thi trj_out.gro contain broken POPC molecules > Pls suggest me what options I have to use for -pbc? or any addition option I > have to use? > Thanks in advance... > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] problem with trjconv
Hi all, I am trying to use *trjconv command for -pbc but POPC molecules are breaking when visualize in VMD. The commands used are grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or whole Thi trj_out.gro contain broken POPC molecules Pls suggest me what options I have to use for -pbc? or any addition option I have to use? Thanks in advance... ___ 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] Problem with trjconv
Hi Aline, You probably missed the part of David's answer that this was probably fixed in CVS code already? In that case: This has probably been fixed in CVS code already. Some silly bug, no particular reasons not to give you a frame at 100ps. Tsjerk On 4/25/07, Aline Rossi <[EMAIL PROTECTED]> wrote: I have a 100ps .trr file. If I use: trjconv -f in.trr -o out.gro -dump 95 -s in.tpr trjconv stops returning the following warning: "Reading frame 20 time 95.000 WARNING no output, trajectory ended at 100" Same warning if I -dump with any other value, as well with -b 95 -e 95. Why does the trjconv does not give me the output file? The gromacs version is 3.3.1. Thanks for your help. Aline Rossi ___ 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
[gmx-users] Problem with trjconv
* **I have a 100ps .trr file. If I use: **trjconv -f in.trr -o out.gro -dump 95 -s in.tpr ** **trjconv stops returning the following warning: **"Reading frame 20 time 95.000 ** **WARNING no output, trajectory ended at 100" ** ** **Same warning if I -dump with any other value, as well with -b 95 -e 95. ** **Why does the trjconv does not give me the output file? The gromacs version is 3.3.1. ** **Thanks for your help. ** **Aline Rossi* ___ 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] Problem with trjconv
Aline wrote: * Greetings, *>* *>* I have a 100ps .trr file. If I use: *>* trjconv -f in.trr -o out.gro -dump 95 -s in.tpr *>* *>* trjconv stops returning the following warning: *>* "Reading frame 20 time 95.000 *>* *>* WARNING no output, trajectory ended at 100" *>* *>* *>* Same warning if I -dump with any other value, as well with -b 95 -e 95. *>* *>* Why does the trjconv does not give me the output file? *>* *>* Thanks for your help. *>* *>* Aline *>* *>* *David wrote: Which gromacs version? This has probably been fixed in the development code already. -- David. The gromacs version is 3.3.1. Aline ___ 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] Problem with trjconv
Aline wrote: Greetings, I have a 100ps .trr file. If I use: trjconv -f in.trr -o out.gro -dump 95 -s in.tpr trjconv stops returning the following warning: "Reading frame 20 time 95.000 WARNING no output, trajectory ended at 100" Same warning if I -dump with any other value, as well with -b 95 -e 95. Why does the trjconv does not give me the output file? Thanks for your help. Aline Which gromacs version? This has probably been fixed in the development code already. -- 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] Problem with trjconv
Greetings, I have a 100ps .trr file. If I use: trjconv -f in.trr -o out.gro -dump 95 -s in.tpr trjconv stops returning the following warning: "Reading frame 20 time 95.000 WARNING no output, trajectory ended at 100" Same warning if I -dump with any other value, as well with -b 95 -e 95. Why does the trjconv does not give me the output file? Thanks for your help. Aline ___ 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] problem with trjconv
OZGE ENGIN wrote: Hi, First of all, thank you for your attention. I used g_hbond in order to analyze hydrogen bonds formed;but, I need a more detailed information. The command that you mentioned is capable of giving information about hydrogen bonds formed in each frame. However, I want to investigate the exact donor and acceptor groups in each frame. In this respect, I converted the xtc file to a pdb file to get all of the coordinates of both water and protein molecules. What should I do? Gee I sound like a broken record. Have you looked at "man g_hbond" to see all of its options? 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: Re: [gmx-users] problem with trjconv
Hi, First of all, thank you for your attention. I used g_hbond in order to analyze hydrogen bonds formed;but, I need a more detailed information. The command that you mentioned is capable of giving information about hydrogen bonds formed in each frame. However, I want to investigate the exact donor and acceptor groups in each frame. In this respect, I converted the xtc file to a pdb file to get all of the coordinates of both water and protein molecules. What should I do? Thanks in advance Ozge -Original Message- From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Date: Wed, 28 Feb 2007 17:52:34 +0100 Subject: Re: [gmx-users] problem with trjconv Hi Ozge, Why do you first want to go to a .pdb trajectory? Gromacs comes with g_hbond, which can analyze hydrogen bonds for you, as well as giving you an index file containing the atoms involved in hydrogen bonds, which you can use to extract those from your trajectory. In addition, g_hbond also does "normal" contacts, other than hydrogen bonds. Tsjerk On 2/28/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > OZGE ENGIN wrote: > > Hi, > > > > I have a problem with the trjconv command. > > > > I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed > > between protein and water molecules. In this respect, I converted the xtc > > file into a pdb file by selecting system option. As you can understand the > > overall file was such a large file that I could not handle it. So, I want > > to know whether there is any possibility to select water molecules within a > > cutoff value or to extract frames within given time steps? For instance, > > at every 70 th step, from 70 ps to 80 ps. > > If you read the man page for trjconv, you will see an option to do the > latter. I don't think the former is implemented in the gromacs utilities. > > 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 > -- 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 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] problem with trjconv
Hi Ozge, Why do you first want to go to a .pdb trajectory? Gromacs comes with g_hbond, which can analyze hydrogen bonds for you, as well as giving you an index file containing the atoms involved in hydrogen bonds, which you can use to extract those from your trajectory. In addition, g_hbond also does "normal" contacts, other than hydrogen bonds. Tsjerk On 2/28/07, Mark Abraham <[EMAIL PROTECTED]> wrote: OZGE ENGIN wrote: > Hi, > > I have a problem with the trjconv command. > > I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within given time steps? For instance, at every 70 th step, from 70 ps to 80 ps. If you read the man page for trjconv, you will see an option to do the latter. I don't think the former is implemented in the gromacs utilities. 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 -- 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 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 trjconv
OZGE ENGIN wrote: Hi, I have a problem with the trjconv command. I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within given time steps? For instance, at every 70 th step, from 70 ps to 80 ps. If you read the man page for trjconv, you will see an option to do the latter. I don't think the former is implemented in the gromacs utilities. 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
[gmx-users] problem with trjconv
Hi, I have a problem with the trjconv command. I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within given time steps? For instance, at every 70 th step, from 70 ps to 80 ps. Thanks in advance Ozge ___ 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 trjconv centering after fitting
Thanks Tsjerk, that works great! Also your explaination was very clear. I would just like to follow up that what works for me was (2 steps): trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans I now understand also why the following single step conversion doesn't work, but perhaps this following combination should be disallowed by trjconv or the code should be changed to do the rotation as the last step: trjconv -s a.tpr -f a.xtc -o c.xtc -center tric -ur compact -fit rot+trans -pbc inbox > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Problem with trjconv centering after fitting > To: "Discussion list for GROMACS users" > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > Would that be the same? What happened here is that the system was > first fitted. Thus, the system is rotated and any operation concerning > pbc after that point will be screwed up, because the box definition > does not match the system. Solution: first perform all operations > involving pbc, then fit the system. Note that translations are not a > problem, only rotations. An alternative solution would be to have all > routines involving rotation of the frame also rotating the box > definition in that frame in the trajectory. But this requires > modifications in many routines. > > Tsjerk > > On 8/28/06, David van der Spoel <[EMAIL PROTECTED]> wrote: > > [EMAIL PROTECTED] wrote: > > > Starting from a rhombic dodecahedron xtc file, > > > > > > trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc > > > trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc > > > > > > Visualization of a.xtc and a_fit.xtc via VMD are as expected. > Nevertheless, > > > a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why > is this? > > > > > > ___ > > > 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 > > could this be the same problem as reported here: > > > > http://bugzilla.gromacs.org/show_bug.cgi?id=99 > > > > -- > > 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 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, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > > > -- > > ___ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > > > End of gmx-users Digest, Vol 28, Issue 81 > * > ___ 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 trjconv centering after fitting
Hi, Would that be the same? What happened here is that the system was first fitted. Thus, the system is rotated and any operation concerning pbc after that point will be screwed up, because the box definition does not match the system. Solution: first perform all operations involving pbc, then fit the system. Note that translations are not a problem, only rotations. An alternative solution would be to have all routines involving rotation of the frame also rotating the box definition in that frame in the trajectory. But this requires modifications in many routines. Tsjerk On 8/28/06, David van der Spoel <[EMAIL PROTECTED]> wrote: [EMAIL PROTECTED] wrote: > Starting from a rhombic dodecahedron xtc file, > > trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc > trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc > > Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless, > a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why is this? > > ___ > 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 could this be the same problem as reported here: http://bugzilla.gromacs.org/show_bug.cgi?id=99 -- 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 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, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ 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 trjconv centering after fitting
[EMAIL PROTECTED] wrote: Starting from a rhombic dodecahedron xtc file, trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless, a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why is this? ___ 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 could this be the same problem as reported here: http://bugzilla.gromacs.org/show_bug.cgi?id=99 -- 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 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 trjconv centering after fitting
Starting from a rhombic dodecahedron xtc file, trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless, a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why is this? ___ 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
