[gmx-users] Windows 7
Hi, Is this software compatible with windows 7. Thanks. Regards, Chathurika. -- 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] Windows 7
On 19/06/2011 6:34 PM, Chathurika Abeyrathne wrote: Hi, Is this software compatible with windows 7. Yes, but its not really a desirable platform for serious computation. See http://www.gromacs.org/Downloads/Installation_Instructions/Windows for instructions to build it. 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
Re: [gmx-users] cross correlations
Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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] cross correlations
Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] cross correlations
Hi, Thats actualy that i did here [1]. Extracting coordinate for every atom in interesting two group and computing C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is vectors [1] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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] cross correlations
Of course you did... Though mind the brackets :) C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) The point I want to make is that you can easily take the output from g_covar -ascii and turn it into a correlation matrix. In R (r-project.org) there is even a dedicated function for it: x - scan(covar.dat) x - matrix(x,sqrt(length(x))) y - cov2cor(x) write(y,correl.dat,ncolumns=3) Cheers, Tsjerk On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi, Thats actualy that i did here [1]. Extracting coordinate for every atom in interesting two group and computing C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is vectors [1] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] reg g_hbond
Dear Justin, Thank you for your previous reply Dear Justin I used g_hbond tool i have got .xvg file In that file there are three column The second and third colum represents What ?. Which column represents total no of Hbonds throught the entire trajectory and which Columns represents Average number of H bonds Thanks in Advance -- 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] reg g_hbond
On 19/06/2011 11:44 PM, vidhya sankar wrote: Dear Justin, Thank you for your previous reply Dear Justin I used g_hbond tool i have got .xvg file In that file there are three column The second and third colum represents What ?. Which column represents total no of Hbonds throught the entire trajectory and which Columns represents Average number of H bonds Thanks in Advance Look at the legend text in the .xvg file. Also, try Google before emailing - often fruitful: http://www.google.com.au/search?sourceid=chromeie=UTF-8q=gromacs+g_hbond+output http://www.google.com.au/search?sourceid=chromeie=UTF-8q=gromacs+g_hbond+output 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] is lincs used with virtual hydrogens?
Thank you Mark, I really appreciate it. -- original message -- On 20/06/2011 1:23 AM, chris.neale at utoronto.ca wrote: Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. No... my second email observed that LINCS warnings can result when v-sites are being used, and I ascribed that effect to the size of the time step. I didn't say v-sites were doing anything with angle constraints. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Therefore (A): pdb2gmx -vsite none constraints = h-angles constraint_algorithm = lincs -- P-LINCS constrains all bonds and angles involving hydrogens But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds constraint_algorithm = lincs -- Hydrogens are built as V-sites and P-LINCS constrains all bonds that do not involve hydrogen. Of course, water is treated by SETTLE in both of the above. Please note that I am not concerned about getting LINCS warnings. I probably should not have mentioned that. I am simply trying to figure out exactly how to write my methods section. Both the above are correct understandings. I think you misread my second email. I'd intended to put my parenthetical observation about LINCS in the first email, but forgot to (however you seem to have understood my context fine). Sorry for whatever. :) 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
Re: [gmx-users] is lincs used with virtual hydrogens?
On 20/06/2011 1:23 AM, chris.ne...@utoronto.ca wrote: Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. No... my second email observed that LINCS warnings can result when v-sites are being used, and I ascribed that effect to the size of the time step. I didn't say v-sites were doing anything with angle constraints. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Therefore (A): pdb2gmx -vsite none constraints = h-angles constraint_algorithm = lincs -- P-LINCS constrains all bonds and angles involving hydrogens But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds constraint_algorithm = lincs -- Hydrogens are built as V-sites and P-LINCS constrains all bonds that do not involve hydrogen. Of course, water is treated by SETTLE in both of the above. Please note that I am not concerned about getting LINCS warnings. I probably should not have mentioned that. I am simply trying to figure out exactly how to write my methods section. Both the above are correct understandings. I think you misread my second email. I'd intended to put my parenthetical observation about LINCS in the first email, but forgot to (however you seem to have understood my context fine). Sorry for whatever. :) 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] is lincs used with virtual hydrogens?
Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Therefore (A): pdb2gmx -vsite none constraints = h-angles constraint_algorithm = lincs -- P-LINCS constrains all bonds and angles involving hydrogens But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds constraint_algorithm = lincs -- Hydrogens are built as V-sites and P-LINCS constrains all bonds that do not involve hydrogen. Of course, water is treated by SETTLE in both of the above. Please note that I am not concerned about getting LINCS warnings. I probably should not have mentioned that. I am simply trying to figure out exactly how to write my methods section. Thank you, Chris. -- original message -- Mark On Sat, Jun 18, 2011 at 4:40 PM, chris.neale at utoronto.ca mailto:chris.neale at utoronto.ca chris.neale at utoronto.ca mailto:chris.neale at utoronto.ca wrote: Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination that I have never tried) But when I use (B): pdb2gmx -vsite hydrogen constraints = all-bonds It seems possible to me that LINCS is not used but instead the position of the atom is simply built from a mathematical function. Perhaps this all stems from my lack of thorough understanding of LINCS, but it seems to me that there need be no iteration to simply place an atoms based on virtual_sites3 (which are constructed by pdb2gms -hydrogen) For now, I'll simply add a line to state that I built virtual sites for hydrogen atoms to make it clear, but I'd still like to understand the difference between options A and B, above, if you have some time. Thank you again, Chris. On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at utoronto.ca http://utoronto.ca chris.neale at utoronto.ca http://utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but that warning message could possibly have been written with the assumption that I used LINCS and not virtual hydrogens. Probably. To make sure check the constraint-algorithm selected in your mdp. BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6. Finally, is there a method that needs to be named or cited in relation to the fact that the angles are now constrained? Is that also done with P-LINCS? This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites. Roland Thank you, Chris. -- 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: local pressure v4.5 issues
Dear all, I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable. I am not sure how to figure out what goes wrong with my previous simulations when plugged into the local pressure gromacs. Could someone help me in figuring out whats the issue ? Thank You. On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote: Dear all, I installed the git version of local pressure calculation from http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure The I invoked mdrun mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1 This created a file named localpressure.dat0. This is a binary file so I could not look at it directly. I am not sure if there is a tool in the gromacs to look at it directly. To look at the data in localpressure.dat0 I used the planar_av.c code available in pressure-tools folder at http://md.chem.rug.nl/cgmartini/index.php/3d When I look at the Pressure tensor averaged over xy plane, some of the numbers are reasonable but few of them are ridiculously large numbers which is not expected. I checked this on two different simulations and I got the same problems. The simulations had run OK previously. Could someone help me in figuring our whats going on ? Amit Choubey -- 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] LINCS WARNING relative constraint deviation
Dear all, I am trying to simulate a GB simulation of a 112 amino acid long protein. I keep getting these errors, Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 33.319842, max 438.763717 (between atoms 79 and 81) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.058237, max 1.390675 (between atoms 91 and 93) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 91 92 50.20.1016 0.1065 0.1010 91 93 90.00.1002 0.2415 0.1010 91 94 70.20.1025 0.1066 0.1010 79 80 90.00.1057 1.0667 0.1090 79 81 90.01.3066 47.9342 0.1090 85 86 90.00.1084 0.1758 0.1090 85 87 90.01.0654 0.1668 0.1090 88 89 90.00.1097 0.6994 0.1090 88 90 90.00.1125 0.1097 0.1090 91 92 50.20.1016 0.1065 0.1010 91 93 90.00.1002 0.2415 0.1010 91 94 70.20.1025 0.1066 0.1010 I am copying my mdp parameters below, I'd appreciate any suggestions to fix that. integrator = sd tinit= 0 dt = 0.002 nsteps = 250 simulation_part = 1 init_step= 1 nstxout = 5000 nstvout = 5000 nstenergy= 500 nstxtcout= 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode= Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist= 2.0 implicit_solvent = GBSA gb_algorithm = OBC gb_saltconc = 0.15 rgbradii = 2.0 coulombtype = Cut-off fourierspacing = 0.1 pme_order= 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; velocity temperature control gen_vel = yes gen_temp = 300.0 annealing= no constraints = hbonds constraint_algorithm = lincs morse= no Thanks, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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: LINCS WARNING relative constraint deviation
I also checked the output of the minimization: Steepest Descents converged to machine precision in 402 steps, but did not reach the requested Fmax 10. Potential Energy = -1.81875038188621e+04 Maximum force = 3.20769543152855e+02 on atom 331 Norm of force = 2.04356801849931e+01 I assume the structure is not relaxed enough to start a simulation. How can I get it minimize further? I increased the step size up to 0.1 ps, i still get the same result. Thanks, Nihal On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz enihalkork...@gmail.comwrote: Dear all, I am trying to simulate a GB simulation of a 112 amino acid long protein. I keep getting these errors, Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 33.319842, max 438.763717 (between atoms 79 and 81) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.058237, max 1.390675 (between atoms 91 and 93) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 91 92 50.20.1016 0.1065 0.1010 91 93 90.00.1002 0.2415 0.1010 91 94 70.20.1025 0.1066 0.1010 79 80 90.00.1057 1.0667 0.1090 79 81 90.01.3066 47.9342 0.1090 85 86 90.00.1084 0.1758 0.1090 85 87 90.01.0654 0.1668 0.1090 88 89 90.00.1097 0.6994 0.1090 88 90 90.00.1125 0.1097 0.1090 91 92 50.20.1016 0.1065 0.1010 91 93 90.00.1002 0.2415 0.1010 91 94 70.20.1025 0.1066 0.1010 I am copying my mdp parameters below, I'd appreciate any suggestions to fix that. integrator = sd tinit= 0 dt = 0.002 nsteps = 250 simulation_part = 1 init_step= 1 nstxout = 5000 nstvout = 5000 nstenergy= 500 nstxtcout= 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode= Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist= 2.0 implicit_solvent = GBSA gb_algorithm = OBC gb_saltconc = 0.15 rgbradii = 2.0 coulombtype = Cut-off fourierspacing = 0.1 pme_order= 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; velocity temperature control gen_vel = yes gen_temp = 300.0 annealing= no constraints = hbonds constraint_algorithm = lincs morse= no Thanks, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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
