[gmx-users] Re: g_density fails after calculating for the last snapshot
Hi All Thanks to Christopher Neale for his comments. There was a frame missing. But the frame was nowhere near the end. I played around with the trajectory and timestamps, got rid of that frame and obtained the density. Interestingly, g_density in version 4.5.4 was able to run the .xtc. It mentioned that there was a frame missing, but it gave me the right output. On Fri, Mar 8, 2013 at 9:25 PM, Christopher Neale [via GROMACS] ml-node+s5086n5006228...@n6.nabble.com wrote: What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ? Also, can you extract that problematic frame with trjconv and run g_density on that one frame (what happens?). Also, can you make a new .xtc that is missing that last frame and see what g_density does? These will help you to figure out what is going on. Chris. -- original message -- Hi All I have a 100 ns lipid simulation for which I want the density profile. I issued the following command g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5 The program fails with the following message Selected 3: 'Water' Last frame 25000 time 10.000 *** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x00d655d0 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb120a73b96] /usr/lib/libgmxana.so.6(calc_density+0x30c)[0x7fb120e14bec] /usr/lib/libgmxana.so.6(gmx_density+0x42b)[0x7fb120e1541b] g_density(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb120a1676d] g_density[0x400659] === Memory map: 0040-00401000 r-xp 08:06 4099695 /usr/bin/g_density 0060-00601000 r--p 08:06 4099695 /usr/bin/g_density 00601000-00602000 rw-p 1000 08:06 4099695 /usr/bin/g_density 00d57000-00e57000 rw-p 00:00 0 [heap] 7fb11f003000-7fb11f018000 r-xp 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f018000-7fb11f217000 ---p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f217000-7fb11f218000 r--p 00014000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f218000-7fb11f219000 rw-p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f239000-7fb11f26c000 rw-p 00:00 0 7fb11f26c000-7fb11f282000 r-xp 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f282000-7fb11f481000 ---p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f481000-7fb11f482000 r--p 00015000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f482000-7fb11f483000 rw-p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f483000-7fb11f485000 r-xp 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f485000-7fb11f685000 ---p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f685000-7fb11f686000 r--p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f686000-7fb11f687000 rw-p 3000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f687000-7fb11f7d8000 r-xp 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f7d8000-7fb11f9d7000 ---p 00151000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9d7000-7fb11f9df000 r--p 0015 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9df000-7fb11f9e1000 rw-p 00158000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9e1000-7fb11f9e2000 rw-p 00:00 0 7fb11f9e2000-7fb11fb46000 r-xp 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fb46000-7fb11fd45000 ---p 00164000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd45000-7fb11fd51000 r--p 00163000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd51000-7fb11fd52000 rw-p 0016f000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd52000-7fb11fe4d000 r-xp 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb11fe4d000-7fb12004c000 ---p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004c000-7fb12004d000 r--p 000fa000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004d000-7fb12004e000 rw-p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004e000-7fb120066000 r-xp 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120066000-7fb120265000 ---p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120265000-7fb120266000 r--p 00017000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120266000-7fb120267000 rw-p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120267000-7fb12026b000 rw-p 00:00 0 7fb12026b000-7fb1204f9000 r-xp 08:06 4099651 /usr/lib/libgmx.so.6 7fb1204f9000-7fb1206f8000 ---p 0028e000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206f8000-7fb1206fe000 r--p 0028d000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206fe000-7fb120707000 rw-p 00293000 08:06 4099651 /usr/lib/libgmx.so.6
[gmx-users] Re: gromacs VERSION 4.0.7-There is no domain decomposition.....
Dear Christoph thanks for quick reply It seems like mdrun was not able to find a decomposition automatically, try to give one by hand: $ mdrun -dd 2 2 4 this command is general or not? Btw, your gromacs is 2 major versions behind, it might be a good idea to update yes, but I modify some force field in this versiom nad need to work with it do you think I go to new version, don't get this error? Best Regards Hamid Mosaddeghi -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006247p5006251.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] Re: gromacs VERSION 4.0.7-There is no domain
Date: Sun, 10 Mar 2013 03:17:24 -0700 (PDT) From: Hamid Mosaddeghi hamid5920...@yahoo.com Subject: [gmx-users] Re: gromacs VERSION 4.0.7-There is no domain decomposition. To: gmx-users@gromacs.org Message-ID: 1362910644976-5006251.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Dear Christoph thanks for quick reply It seems like mdrun was not able to find a decomposition automatically, try to give one by hand: $ mdrun -dd 2 2 4 this command is general or not? No, it is not general, but you wanted to run on 16 cores, so a decomposition of 2x2x4 (=16 and 4 in z as the box was the longest in z) would work. Btw, your gromacs is 2 major versions behind, it might be a good idea to update yes, but I modify some force field in this versiom nad need to work with it If this change is of general interest, create a patch and submit it here: https://gerrit.gromacs.org/ do you think I go to new version, don't get this error? Many many things has been improved from 4.0 to 4.6, so I think it is save to say it will most likely work. Best Regards Hamid Mosaddeghi -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006247p5006251.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- -- 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! End of gmx-users Digest, Vol 107, Issue 42 ** -- Christoph Junghans Web: http://www.compphys.de -- 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] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)
Dear, This is the same issue that I asked last time. I wonder (1) if I setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even though the conformation of a protein is in equilibrium in the enough degree, or (2) if it gromacs does not make it in equilibrium because of the limit of the tolerance that gromacs can take care of. Is there anyone who can give me an advice for this? I updated the sample location in the case that the previous Skype link is not available. I am studying several protein fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I found out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues even though having 6 zero eigenvalues are expected. I tried to reduce the tolerance level lesser than 10^-6 for the l-bfgs minimization, but still it have only 4 zero eigenvalues. Following is the 9 smallest eigenvalues (you can see that it has only 4 close-to-zero eigenvalues): -1.8476593e-06-1.2164109e-06-1.4830436e-071.3104790e-061.1364704e+001.7418209e+002.2836573e+003.7218206e+004.4875873e+00 Theoretically, NMA should have 6 zero eigenvalues which represents the freedom of the rotation and translation. I wonder why this happens. Is there anyone who can help me for this problem? In order to specify the case, I leave a link to download a zip file that contains files for one NMA tests having the problem: script, mdp, pdb, gro, topol, etc. The zip file also includes the eigenvalue/vector files. http://129.186.69.109/NMA-test.zip Thank you very much. -- Hyuntae -- 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] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)
I can imagine why you would go past the first few, but does it print the zero's or just negate them from the equation, as there 0? Stephan Original-Nachricht Datum: Sun, 10 Mar 2013 14:34:52 -0500 Von: Hyuntae Na h...@hotmail.com An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs) Dear, This is the same issue that I asked last time. I wonder (1) if I setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even though the conformation of a protein is in equilibrium in the enough degree, or (2) if it gromacs does not make it in equilibrium because of the limit of the tolerance that gromacs can take care of. Is there anyone who can give me an advice for this? I updated the sample location in the case that the previous Skype link is not available. I am studying several protein fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I found out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues even though having 6 zero eigenvalues are expected. I tried to reduce the tolerance level lesser than 10^-6 for the l-bfgs minimization, but still it have only 4 zero eigenvalues. Following is the 9 smallest eigenvalues (you can see that it has only 4 close-to-zero eigenvalues): -1.8476593e-06-1.2164109e-06-1.4830436e-071.3104790e-061.1364704e+001.7418209e+002.2836573e+003.7218206e+004.4875873e+00 Theoretically, NMA should have 6 zero eigenvalues which represents the freedom of the rotation and translation. I wonder why this happens. Is there anyone who can help me for this problem? In order to specify the case, I leave a link to download a zip file that contains files for one NMA tests having the problem: script, mdp, pdb, gro, topol, etc. The zip file also includes the eigenvalue/vector files. http://129.186.69.109/NMA-test.zip Thank you very much. -- Hyuntae -- 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] query regarding mk_angndx
To see how the dihedral is defined you need to look at the topology file, not the coordinate file. Additionally, the name for the index group tells you the type of dihedral. Be careful with that, especially if you are interested in a particular bond and there is another dihedral within the system/molecule that has the same parameters as the script will group them together into one if you are not careful. 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. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Kavyashree M Sent: Sunday, 10 March 2013 2:09 AM To: Discussion list for GROMACS users Subject: [gmx-users] query regarding mk_angndx -- Forwarded message -- From: Kavyashree M hmkv...@gmail.com Date: Fri, Mar 8, 2013 at 10:45 PM Subject: query regarding mk_angndx To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, I used mkang_ndx to create an index file with dihedral angles. Input was: mk_angndx -s a.tpr -n angle.ndx -type dihedral output angle.ndx read like this - [ Phi=180.0_2_43.93 ] 520181922373536273230 31 3959575861767475667169 70 ... According to my understanding the numbers indicate the 4 atoms defining the particular dihedral angle. But when I checked the pdb file for these atoms- ATOM 5 CA MET A 1 111.430 40.170 113.130 1.00 0.00 ATOM 18 C MET A 1 112.060 41.020 112.030 1.00 0.00 ATOM 19 O MET A 1 111.910 42.240 112.010 1.00 0.00 ATOM 20 N GLN A 2 112.940 40.430 111.220 1.00 0.00 I could not make out how this defines phi? Kindly clarify my confusion. Thank you kavya -- 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
