Re: [gmx-users] Re: choice of force field -reg
Dear Sir, Thank you so much for the response. Revathi -- 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
Re: [gmx-users] .GRO Formatting
In GRO file, the atom numbers do not really matter. Just use any number you like. It will work correctly. mdrun will renumber atoms from 9, as it likes, automatically. Dr. Vitaly Chaban On Thu, May 30, 2013 at 4:57 AM, Phil pmcho...@syr.edu wrote: I'm working on a .GRO file and have come across a formatting error. In the manual, it states that the spacing for each column in the .GRO file is: residue number (5 positions, integer) residue name (5 characters) atom name (5 characters) atom number (5 positions, integer) position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places) In my .GRO file, the atom number exceeds 5 positions. How should I reformat the .GRO file to account for this? -- View this message in context: http://gromacs.5086.x6.nabble.com/GRO-Formatting-tp5008625.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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
Re: [gmx-users] .GRO Formatting
Hey, If the gro file was built with a non-gmx program, it may be that the numbers indeed broke the format, which then needs to be fixed. In case you write your own program, you want to use a statement like atid = atid %1e5 to make sure it doesn't go over five digits. Correcting the format is possible, but may become a tiny bit nasty. Cheers, Tsjerk On Thu, May 30, 2013 at 9:09 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: In GRO file, the atom numbers do not really matter. Just use any number you like. It will work correctly. mdrun will renumber atoms from 9, as it likes, automatically. Dr. Vitaly Chaban On Thu, May 30, 2013 at 4:57 AM, Phil pmcho...@syr.edu wrote: I'm working on a .GRO file and have come across a formatting error. In the manual, it states that the spacing for each column in the .GRO file is: residue number (5 positions, integer) residue name (5 characters) atom name (5 characters) atom number (5 positions, integer) position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places) velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places) In my .GRO file, the atom number exceeds 5 positions. How should I reformat the .GRO file to account for this? -- View this message in context: http://gromacs.5086.x6.nabble.com/GRO-Formatting-tp5008625.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] Vritual Sites and simulation time-step
Manual 6.7? On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce number of atoms of the some solvent-like molecule or to mimic electron pairs in the water for instance) influence on time-step can be achieved ? James -- 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 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
Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field
No charges = no problem. You can trivially test this yourself with mdrun -rerun ;-) Manual 4.1.4 talks about what RF is doing. Mark On Thu, May 30, 2013 at 6:38 AM, Dallas Warren dallas.war...@monash.eduwrote: In a system that has no charges, should we observe a difference between simulations using PME/Cut-offs or Reaction Field? From my understanding there should not be, since there are no charges which treatment you use shouldn't' make a difference. However, it does and I am trying to work out why. Any suggestions on the reason? What is it that Reaction Field is doing, does it influence anything other than long range charge interactions? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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 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
Re: [gmx-users] Vritual Sites and simulation time-step
Mark, thanks for advise. As I understood for the usage of virtual sites in typical protein-water system I should (1) define all hydrogens as the virtual atoms (2) increase atom masses of the hydrogens presented in the water, COOH NH2 OH and SH as well as polar groups (3) make virtual sites for the angles and dihedrals of peptide bond as well as sidechains. Also I've noticed that (1) and (2) can be done with the pdb2gmx with options -vsite and -heavyh respectfully. From this point its not quite clear for me (1) should I make some corrections in topology for dihedrals? In the manual 6.7 I've found some suggestions for the dihedrals of the different functional groups. (2) should I define VSITES for solvent molecules filled into the box by the genbox ? (3) As I understood the inclusion of the VSITES for hydrogens would allow me to increase timestep up to 5-8fs. What possible negative side-effects of the inclusion of VSITES might occur in simulation ? James 2013/5/30 Mark Abraham mark.j.abra...@gmail.com Manual 6.7? On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce number of atoms of the some solvent-like molecule or to mimic electron pairs in the water for instance) influence on time-step can be achieved ? James -- 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 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 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] Overlap between PC motions
Dear all, I posted some days ago an issue regarding overlap values. If any of you is experienced with this I would appreciate some comments. Please find below the mentioned post: I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot Regards, Miguel -- 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
Re: [gmx-users] Vritual Sites and simulation time-step
Also some questions about corrections in the mdp besides the time-step file which should be included with the VS. 1) What constrains algorithm should I use ? typically I use ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy 2) Should I vary tau_t constant assuming that I use SD integrator as the thermostat ( I'm using 2 ps ) ? 2013/5/30 James Starlight jmsstarli...@gmail.com Mark, thanks for advise. As I understood for the usage of virtual sites in typical protein-water system I should (1) define all hydrogens as the virtual atoms (2) increase atom masses of the hydrogens presented in the water, COOH NH2 OH and SH as well as polar groups (3) make virtual sites for the angles and dihedrals of peptide bond as well as sidechains. Also I've noticed that (1) and (2) can be done with the pdb2gmx with options -vsite and -heavyh respectfully. From this point its not quite clear for me (1) should I make some corrections in topology for dihedrals? In the manual 6.7 I've found some suggestions for the dihedrals of the different functional groups. (2) should I define VSITES for solvent molecules filled into the box by the genbox ? (3) As I understood the inclusion of the VSITES for hydrogens would allow me to increase timestep up to 5-8fs. What possible negative side-effects of the inclusion of VSITES might occur in simulation ? James 2013/5/30 Mark Abraham mark.j.abra...@gmail.com Manual 6.7? On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce number of atoms of the some solvent-like molecule or to mimic electron pairs in the water for instance) influence on time-step can be achieved ? James -- 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 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 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
Re: [gmx-users] Overlap between PC motions
Hi Miguel, Sorry for not responding earlier, but the question isn't really simple :) What you do is determining the covariance matrix from the start up to a certain point and see for different end points what the overlap is with the covariance matrix from the whole. This means that in all cases, the relaxation of the system is included, and this is the dominant contribution to your covariance matrix. At some point, the system has reached the region around B and then stays there. All kinds of things may be happening, but they're overwhelmed by the changes associated with the relaxation. Hence, the part of the trajectory after 70 ns doesn't contribute significantly to the covariance matrix anymore. Hope it helps, Tsjerk On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García mig.momp...@gmail.com wrote: Dear all, I posted some days ago an issue regarding overlap values. If any of you is experienced with this I would appreciate some comments. Please find below the mentioned post: I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot Regards, Miguel -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field
Hmmm... And what does the observed difference look like, numerically? On Thu, May 30, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.comwrote: No charges = no problem. You can trivially test this yourself with mdrun -rerun ;-) Manual 4.1.4 talks about what RF is doing. Mark On Thu, May 30, 2013 at 6:38 AM, Dallas Warren dallas.war...@monash.edu wrote: In a system that has no charges, should we observe a difference between simulations using PME/Cut-offs or Reaction Field? From my understanding there should not be, since there are no charges which treatment you use shouldn't' make a difference. However, it does and I am trying to work out why. Any suggestions on the reason? What is it that Reaction Field is doing, does it influence anything other than long range charge interactions? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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 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 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
Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field
Things should be identical - any quantity computed from a zero charge has to be zero :-). Mark On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hmmm... And what does the observed difference look like, numerically? On Thu, May 30, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: No charges = no problem. You can trivially test this yourself with mdrun -rerun ;-) Manual 4.1.4 talks about what RF is doing. Mark On Thu, May 30, 2013 at 6:38 AM, Dallas Warren dallas.war...@monash.edu wrote: In a system that has no charges, should we observe a difference between simulations using PME/Cut-offs or Reaction Field? From my understanding there should not be, since there are no charges which treatment you use shouldn't' make a difference. However, it does and I am trying to work out why. Any suggestions on the reason? What is it that Reaction Field is doing, does it influence anything other than long range charge interactions? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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 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 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 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
Re: [gmx-users] Overlap between PC motions
Hi Tsjerk, Thanks for the reply! So, let me see if I am getting the things right. The same fitting structure is used for the overlap calculation. Since the averaged structure is used for the covariance matrices, this is the reason why the relaxation is included. Am I right? The overall behavior of the system is that the structure keeps very compact and one additional hydrogen bond between two residues is formed at ~60ns, and stable till the end of the run, as computed with g_hbond. That interaction is already present in the average structure. So if I understood properly your comment, from the time window 0-70 up to the end, there will not be significant contributions to the covariance matrix. Thanks for your valuable comments. Highly appreciated! 2013/5/30 Tsjerk Wassenaar tsje...@gmail.com Hi Miguel, Sorry for not responding earlier, but the question isn't really simple :) What you do is determining the covariance matrix from the start up to a certain point and see for different end points what the overlap is with the covariance matrix from the whole. This means that in all cases, the relaxation of the system is included, and this is the dominant contribution to your covariance matrix. At some point, the system has reached the region around B and then stays there. All kinds of things may be happening, but they're overwhelmed by the changes associated with the relaxation. Hence, the part of the trajectory after 70 ns doesn't contribute significantly to the covariance matrix anymore. Hope it helps, Tsjerk On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García mig.momp...@gmail.com wrote: Dear all, I posted some days ago an issue regarding overlap values. If any of you is experienced with this I would appreciate some comments. Please find below the mentioned post: I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot Regards, Miguel -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 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
Re: [gmx-users] Overlap between PC motions
Hi Miguel, The fitting doesn't play a role; it's the dynamics of the system in the internal frame. Because the internal frame moves, you fit, so that any contribution due to the rigid body motion is removed. For the rest you have to look at it like this: You start out somewhere and walk (relax) towards some city, several kilometers away. You get there and get lost in the streets, making random walks. Now, what you do with covariance analysis is looking at the displacements around the mean position. Your mean position will lie somewhere between your starting position and the place where you ended up. The deviations from the mean will be dominated by vectors pointing from wherever you are in the city towards your starting point. That will be reflected in the covariance matrix, which doesn't change much, certainly not in terms of the directions of the first few eigenvectors. Probably you're actually more interested in the things you do in the city, your native configuration energy well. But to analyze that, you have to cut off the part of the journey that brought you there. So it makes sense to do the covariance analysis on the last half or quarter of the trajectory. It would also be interesting to check the convergence from the other side of the trajectory, varying the starting point of the analysis, rather than the end point. Hope it helps, Tsjerk On Thu, May 30, 2013 at 1:37 PM, Miguel Ángel Mompeán García mig.momp...@gmail.com wrote: Hi Tsjerk, Thanks for the reply! So, let me see if I am getting the things right. The same fitting structure is used for the overlap calculation. Since the averaged structure is used for the covariance matrices, this is the reason why the relaxation is included. Am I right? The overall behavior of the system is that the structure keeps very compact and one additional hydrogen bond between two residues is formed at ~60ns, and stable till the end of the run, as computed with g_hbond. That interaction is already present in the average structure. So if I understood properly your comment, from the time window 0-70 up to the end, there will not be significant contributions to the covariance matrix. Thanks for your valuable comments. Highly appreciated! 2013/5/30 Tsjerk Wassenaar tsje...@gmail.com Hi Miguel, Sorry for not responding earlier, but the question isn't really simple :) What you do is determining the covariance matrix from the start up to a certain point and see for different end points what the overlap is with the covariance matrix from the whole. This means that in all cases, the relaxation of the system is included, and this is the dominant contribution to your covariance matrix. At some point, the system has reached the region around B and then stays there. All kinds of things may be happening, but they're overwhelmed by the changes associated with the relaxation. Hence, the part of the trajectory after 70 ns doesn't contribute significantly to the covariance matrix anymore. Hope it helps, Tsjerk On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García mig.momp...@gmail.com wrote: Dear all, I posted some days ago an issue regarding overlap values. If any of you is experienced with this I would appreciate some comments. Please find below the mentioned post: I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot Regards, Miguel -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Increasing performance of siumulation in cluster
Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- 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] how to distribute CPU in GPU workstation?
Dear: I've got 4 GPU in one GPU workstation. I've submit one of my job by command: mdrun -s md.tpr -gpu_id 01 -n -x md.xtc I found that all the 24 CPU were occupied by this job. However, I would like to submit another job with -gpu_id 23, how should I specify the CPU for each job? thank you very much best Albert -- 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] umbrella sampling for two polymer interaction
Dear All, I want to do Umbrella sampling between two different polymers (A and B) interacting with each other with starting configuration separated by some distance and I am trying to bring them closer. I have some queries regarding pull inputs: (this is for to run a umbrella sampling at some distance) pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = ??? pull_ngroups= 2? pull_group0 = polymer_B pull_group1 = polymer_A pull_init1 = 0 pull_rate1 = 0.0 please suggest for following: 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make it interact with some directional vector 2) Which should be group0 or group1, in other words should I pull both together or how I should decide which one should be reference and which to be pulled as both are different polymers? 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 4) I am not able to understand pull_start option with pull_init1. In this case if it is set to yes and 0.0 respectively then does that mean this combination is equivalent to pull_start = No if I just assume pull_init1 does not have any default value (which is 0.0); not existing 5) Also finally where are upper and lower bounds defined. pull_k1 = 1000 is harmonic applied to some equilibrium distance value. How this distance is taken by the programme (or it is just the starting distance taken between two groups) and what are the +/- values defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is assumed equilibrium value and r1 is lower and r4 is upper value which defines shape of potential) thanks, Jiom -- 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] Re: initial temperature ridiculously high
Hi Guozhen, I know it has been a while, BUT I am having same/similar problem with CLAYFF. I start with a configuration optimised by CASTEP. Have you found a solution? Did you continue using CLAYFF? I have a ClayFF.ff available, if you want to compare. Thanks,V -- View this message in context: http://gromacs.5086.x6.nabble.com/initial-temperature-ridiculously-high-tp4453069p5008641.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] About Compiler Option
Dear Justin and other gromacs users , Thank you for your Previous reply I Have AMD Block Edition FX8350 Processor Also I have Ubuntu 10.04 OS Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) As you mailed me for the aforesaid about performance I want to Ugrade gcc version 4.7.2 already i had version gcc 4.4.3 When I want to Upgrade But Though I give the following Commands add-apt-repository ppa:ubuntu-toolchain-r/test apt-get update apt-get install gcc-4.7 it has not been updated this is confirmed When i check gcc version in terminal -- 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
Re: [gmx-users] About Compiler Option
gcc is probably still your old version. The new one would probably be called gcc-4.7 or similar. Erik On 30 May 2013, at 15:15, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin and other gromacs users , Thank you for your Previous reply I Have AMD Block Edition FX8350 Processor Also I have Ubuntu 10.04 OS Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) As you mailed me for the aforesaid about performance I want to Ugrade gcc version 4.7.2 already i had version gcc 4.4.3 When I want to Upgrade But Though I give the following Commands add-apt-repository ppa:ubuntu-toolchain-r/test apt-get update apt-get install gcc-4.7 it has not been updated this is confirmed When i check gcc version in terminal -- 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 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] GROMACS 4.6.2 released
Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6 and 4.6.1. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz Happy simulating! The GROMACS development team -- 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
Re: [gmx-users] GROMACS 4.6.2 released
it seems that Gromacs update quite frequently these days.. On 05/30/2013 05:42 PM, Mark Abraham wrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6 and 4.6.1. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz Happy simulating! The GROMACS development team -- 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
Aw: [gmx-users] umbrella sampling for two polymer interaction
Dear Jiom, Look at justines tutorial, theres example pull .mdp. Stephan Watkins Gesendet:Donnerstag, 30. Mai 2013 um 14:44 Uhr Von:gromacs query gromacsqu...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:[gmx-users] umbrella sampling for two polymer interaction Dear All, I want to do Umbrella sampling between two different polymers (A and B) interacting with each other with starting configuration separated by some distance and I am trying to bring them closer. I have some queries regarding pull inputs: (this is for to run a umbrella sampling at some distance) pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = ??? pull_ngroups = 2? pull_group0 = polymer_B pull_group1 = polymer_A pull_init1 = 0 pull_rate1 = 0.0 please suggest for following: 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make it interact with some directional vector 2) Which should be group0 or group1, in other words should I pull both together or how I should decide which one should be reference and which to be pulled as both are different polymers? 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 4) I am not able to understand pull_start option with pull_init1. In this case if it is set to yes and 0.0 respectively then does that mean this combination is equivalent to pull_start = No if I just assume pull_init1 does not have any default value (which is 0.0); not existing 5) Also finally where are upper and lower bounds defined. pull_k1 = 1000 is harmonic applied to some equilibrium distance value. How this distance is taken by the programme (or it is just the starting distance taken between two groups) and what are the +/- values defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is assumed equilibrium value and r1 is lower and r4 is upper value which defines shape of potential) thanks, Jiom -- 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/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] umbrella sampling for two polymer interaction
Dear Lloyd, I have read that but my system is different regards, On Thu, May 30, 2013 at 8:28 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear Jiom, Look at justines tutorial, there's example pull .mdp. Stephan Watkins *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr *Von:* gromacs query gromacsqu...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] umbrella sampling for two polymer interaction Dear All, I want to do Umbrella sampling between two different polymers (A and B) interacting with each other with starting configuration separated by some distance and I am trying to bring them closer. I have some queries regarding pull inputs: (this is for to run a umbrella sampling at some distance) pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = ??? pull_ngroups = 2? pull_group0 = polymer_B pull_group1 = polymer_A pull_init1 = 0 pull_rate1 = 0.0 please suggest for following: 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make it interact with some directional vector 2) Which should be group0 or group1, in other words should I pull both together or how I should decide which one should be reference and which to be pulled as both are different polymers? 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 4) I am not able to understand pull_start option with pull_init1. In this case if it is set to yes and 0.0 respectively then does that mean this combination is equivalent to pull_start = No if I just assume pull_init1 does not have any default value (which is 0.0); not existing 5) Also finally where are upper and lower bounds defined. pull_k1 = 1000 is harmonic applied to some equilibrium distance value. How this distance is taken by the programme (or it is just the starting distance taken between two groups) and what are the +/- values defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is assumed equilibrium value and r1 is lower and r4 is upper value which defines shape of potential) thanks, Jiom -- 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/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 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 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
Re: [gmx-users] GROMACS 4.6.2 released
Excellent work. Thank you all for working so hard! On Thu, May 30, 2013 at 9:24 PM, Albert mailmd2...@gmail.com wrote: it seems that Gromacs update quite frequently these days.. On 05/30/2013 05:42 PM, Mark Abraham wrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6 and 4.6.1. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/**gromacs/gromacs-4.6.2.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz ftp://ftp.gromacs.org/pub/**manual/manual-4.6.2.pdfftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf http://www.gromacs.org/About_**Gromacs/Release_Notes/**Versions_4.6.2.xhttp://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x http://www.gromacs.org/**Documentation/Installation_**Instructionshttp://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/**files/regressiontests-4.6.2.**tar.gzhttp://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz Happy simulating! The GROMACS development team -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Free energy calculation: merge the topology of 2 molecules
Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B and still maintain a neutral system, the counter-ions have to be transformed too. I tried only transforming only the target molecule not the ions but the simulation crashes very quickly. I searched the gmx-users archives and found some suggestion about merging the topology definition of ions into that of the molecule under one [moleculetype] section. I tried that but mdrun warned me with tons of inconsistent shift: There were 2 inconsistent shifts. Check your topology There were 18 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology There were 12 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology ... and the simulation can't be run in parallel because mdrun would just quick and complain about not being able to do domain decomposition: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 29.6188 nm I guess the issue is Gromacs thinks those counter-ions belongs chemically to the target molecule although they are actually not in close proximity in space, which mess up the DD. partition. I wonder if there's a way to get around that. Thanks, Dejun -- 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
Aw: [gmx-users] Free energy calculation: merge the topology of 2 molecules
Ive had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked, there might be better suggestions though. Stephan Gesendet:Donnerstag, 30. Mai 2013 um 20:48 Uhr Von:Dejun Lin dejun@gmail.com An:gmx-users@gromacs.org Betreff:[gmx-users] Free energy calculation: merge the topology of 2 molecules Hi all, Im trying to set-up a free energy calculation where a molecule has +2 charge in its native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B and still maintain a neutral system, the counter-ions have to be transformed too. I tried only transforming only the target molecule not the ions but the simulation crashes very quickly. I searched the gmx-users archives and found some suggestion about merging the topology definition of ions into that of the molecule under one [moleculetype] section. I tried that but mdrun warned me with tons of inconsistent shift: There were 2 inconsistent shifts. Check your topology There were 18 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology There were 12 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology ... and the simulation cant be run in parallel because mdrun would just quick and complain about not being able to do domain decomposition: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 29.6188 nm I guess the issue is Gromacs thinks those counter-ions belongs chemically to the target molecule although they are actually not in close proximity in space, which mess up the DD. partition. I wonder if theres a way to get around that. Thanks, Dejun -- 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/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] AMBER99sb-ILDN charges for C-terminus GLY with COOH capping
Hello all, I am using pdb2gmx (4.5.5 version) to create an AMBER99sb-ILDN topology file for a peptide. It gives me only NH3+ as the N-terminus and COO- as the C-terminus. But, I want to have the C-terminus as COOH. The C-terminal residue is GLY. Can anybody give me some idea how to get the GLY COOH C-terminus using this force-field? What could be the charges for the terminus? Thanks a lot, Santanu -- 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
Re: [gmx-users] GROMACS 4.6.2 released
On Thu, May 30, 2013 at 5:54 PM, Albert mailmd2...@gmail.com wrote: it seems that Gromacs update quite frequently these days.. We try, thanks! :-) The idea is to get these patch releases out more-or-less monthly. This time, we spent several weeks noticing various correctness problems with not-quite-mainstream uses of mdrun that dragged on longer than we initially thought, else you'd have had it sooner. Thanks to all the loyal developers, bug fixers and reviewers, too! Mark -- 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] Re: GROMACS 4.6.2 released
Sorry, the link to the release notes should be http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.2 (Darn, I was hoping for a clean sheet, but at least this time we got to four hours before someone noticed something was wrong!) Mark On Thu, May 30, 2013 at 5:42 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6 and 4.6.1. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz Happy simulating! The GROMACS development team -- 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
Re: [gmx-users] Free energy calculation: merge the topology of 2 molecules
Thanks for your reply, Stephan. Did the molecule you worked with have any atoms that are isolated (non-bonded) to the others? Was the equilibration run in your 1st case just a way to recruit those isolated atoms to the others in the same molecule? I suspect I might need to add artificial bond to connect the counter-ions to the target molecule. In the 2nd case you mentioned, I'm not sure why it would work for you but not me because I essentially have every atoms in their single charge groups. Thanks, Dejun 2013/5/30 lloyd riggs lloyd.ri...@gmx.ch I've had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked, there might be better suggestions though. Stephan *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr *Von:* Dejun Lin dejun@gmail.com *An:* gmx-users@gromacs.org *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2 molecules Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B and still maintain a neutral system, the counter-ions have to be transformed too. I tried only transforming only the target molecule not the ions but the simulation crashes very quickly. I searched the gmx-users archives and found some suggestion about merging the topology definition of ions into that of the molecule under one [moleculetype] section. I tried that but mdrun warned me with tons of inconsistent shift: There were 2 inconsistent shifts. Check your topology There were 18 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology There were 12 inconsistent shifts. Check your topology There were 16 inconsistent shifts. Check your topology ... and the simulation can't be run in parallel because mdrun would just quick and complain about not being able to do domain decomposition: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 29.6188 nm I guess the issue is Gromacs thinks those counter-ions belongs chemically to the target molecule although they are actually not in close proximity in space, which mess up the DD. partition. I wonder if there's a way to get around that. Thanks, Dejun -- 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/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 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 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
RE: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field
Yes, that is what i thought too. I have one or two things to check, then will report my results. I have been calculating latent heat of vaporisation for a series of alkanes, and the answer is different. Been trying to work out why, if dime setting are wrong etc. Will post my results early next week. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: 30 May 2013 21:31 To: Vitaly Chaban; Discussion list for GROMACS users Subject: Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field Things should be identical - any quantity computed from a zero charge has to be zero :-). Mark On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hmmm... And what does the observed difference look like, numerically? On Thu, May 30, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: No charges = no problem. You can trivially test this yourself with mdrun -rerun ;-) Manual 4.1.4 talks about what RF is doing. Mark On Thu, May 30, 2013 at 6:38 AM, Dallas Warren dallas.war...@monash.edu wrote: In a system that has no charges, should we observe a difference between simulations using PME/Cut-offs or Reaction Field? From my understanding there should not be, since there are no charges which treatment you use shouldn't' make a difference. However, it does and I am trying to work out why. Any suggestions on the reason? What is it that Reaction Field is doing, does it influence anything other than long range charge interactions? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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 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 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 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 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] query on replica exchange
Hi, I am wondering if there is a way I can use twice more number of replica than the number of CPU is available so that each replica will run at 50 % CPU usage..For example if I have 48 replica and have 24 CPUs, is it a possibility to perform Replica exchange in gromacs ? I was using gromacs4.5.4 and I could not get it worked. It works only when I had atleast equal number of Replica and CPU available. Any help will be appreciated. -- 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
