Re: [gmx-users] 1,4-interactions and pairs...again
With no [pairs] section, no 1-4 interactions are computed. Note that gen-pairs=yes does not automatically identifies and add the 1-4 pairs in your system, you need to specify them in the [pair] in your topology. [pairtypes] contain the parameters to build the potential terms for the pairs included in the topology. It works in a similar way as bonds, angles... For each pair listed, grompp look up [pairtypes] to identify the parameters of the 1-4 interactions, if any pair is not present in pairtype directive, an error will come up if gen-pair=no. With gen-pair=yes the potential terms for pairs in the topology which are not under pairtypes are derived using addition rules and fudges. Javier El 15/01/13 23:00, Robson da Silva escribió: Hi gmx users, I'm writing a MD code and, comparing with gromacs, I have some doubts. When I put gen-pairs=yes, fudges=0.5 and no [pairs] or [pairtypes] directives, the program (gmx) would generate 1,4 pairs with the parameters described in the [atomtypes] directive, right? But, at the end of the simulation, I don't see any coul-1,4 or LJ1,4 energy values in the .log file. The 1,4 pairs were generated in this case? Thanks. -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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 generate velocities and gen_temp in mdp files for REMD simulations
Dear Help, I am trying to run REMD simulations and found couple of interesting discussions on GROMACS mailing list regarding ensembles which can be used during REMD. I will be running REMD of small peptide in explicit solvent and I am confused about gen_temp and gen_vel parameters for these simulations below: 1. NPT ensemble at 310 K to get density right. What should be the parameters gen_vel and gen_temp set to? 2. Equilibration at each temperature -NVT ensemble. Although equilibration run will be carried out for a reference temperature range, should the gen_temp still be set to 310K? 3. Replica exchange -What should be gen_temp and gen_velocity set to? Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- 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] multiple pdb of same protein complex
I would like to analyze the different conformations (~1000 structures) of a protein/protein complex using GROMACS. Can I list all of these pdb files within a text file when I start the pdb2gmx; i.e., text file that includes: 0001.pdb 0002.pdb or is there any other ways to handle this problem? many thanks, Serdar -- 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] multiple pdb of same protein complex
You could use a script to do all runs consecutively using one pdb file at a time. Anyway, if what you have are different conformations of the same system, the same topology should apply for all of them, so just need to obtain it once. Javier El 16/01/13 12:07, Serdar Durdagi, PhD escribió: I would like to analyze the different conformations (~1000 structures) of a protein/protein complex using GROMACS. Can I list all of these pdb files within a text file when I start the pdb2gmx; i.e., text file that includes: 0001.pdb 0002.pdb or is there any other ways to handle this problem? many thanks, Serdar -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- 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 Lateral Diffusion of Lipids
Dear Justin Thank you for your Previous reply I am Following your Protein Lipid Tutorial When I do the msd analysis For protein in DPPC lipid-water Bilayer in lateral Z direction using P8 atoms as index Then I have Got the Following Output Is the Following My Out put is Reasonable or Not? Used 101 restart points spaced 10 ps over 1000 ps Fitting from 100 to 900 ps D[ P8] 0.0544 (+/- 0.0057) 1e-5 cm^2/s What Is Lateral Diffusion of Lipids ? Its Value for Membrane Protein (output ) indicates What ? Is there is Limiting (upper, Lower ) Value For Every System ? How could I come to a conclusion That My Value of My Diffusion Coefficient is Reasonable or Not 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] About Lateral Diffusion of Lipids
On 1/16/13 6:18 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply I am Following your Protein Lipid Tutorial When I do the msd analysis For protein in DPPC lipid-water Bilayer in lateral Z direction using P8 atoms as index Then I have Got the Following Output Is the Following My Out put is Reasonable or Not? Literature searching and reading previous studies (both computational and experimental) will tell you whether it's reasonable or not. Used 101 restart points spaced 10 ps over 1000 ps Fitting from 100 to 900 ps D[P8] 0.0544 (+/- 0.0057) 1e-5 cm^2/s Metrics like these require long simulations (tens or hundreds of ns) to be reliable. What Is Lateral Diffusion of Lipids ? Its Value for Membrane Protein (output ) indicates What ? If you don't know what it is, why are you measuring it? Again, do some reading. Is there is Limiting (upper, Lower ) Value For Every System ? How could I come to a conclusion That My Value of My Diffusion Coefficient is Reasonable or Not Same as above. I'm not going to do your homework for you. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs-4.6-beta3 compile warnings intel-suite 2011 and 2013
Hi Ronald, Using intel-suite/64/2013.0/079 with mkl with the release-4-6 branch version: f3dd8cb7ae23accff657551523d05657262a72ff gave no compiler warnings for $ export CC=icc ; export CXX=icpc ; cmake -DGMX_MPI=OFF -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/include -DMKL_LIBRARIES=$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/libmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so -DGMX_OPENMP=ON -DCMAKE_INSTALL_PREFIX=/home/rb1109/libs/gromacs/bin ../ $ make -j8 mdrun $ make install-mdrun Thanks, Richard On 15/01/13 18:42, Roland Schulz wrote: Hi, could you check if you get these warnings also with the latest version from git? We have changed quite a bit sense then. git clone https://gerrit.gromacs.org/p/gromacs git checkout release-4-6 Roland On Tue, Jan 15, 2013 at 9:34 AM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Dear All, I've just installed 4.6-beta3 on my ubuntu linux (Intel Xeon [sandy bridge]) box using both intel-suite/64/2011.10/319, and intel-suite/64/2013.0/079 with mkl Using either compiler I received several hundred warnings of type #120, #167, and #556 (see bellow for examples). I thought this might be vaguely related to Bug #1074, as these all appear to be casting warnings. A small test md simulation ran as expected so the executable seems to be working and it is using AVX_256 acceleration. I therefore don't think this justifies a bug report but I did think it might be worth flagging up that these warnings occur and asking if other people had seen them. If anyone has any recommendations for how to get rid of them or thinks that they are significant I would also be interested. Thanks, Richard my cmake line was: $ export CC=icc ; export CXX=icpc ; cmake -DGMX_MPI=OFF -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/include -DMKL_LIBRARIES=$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/libmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so -DGMX_OPENMP=ON ../ and I then built it with: $ make -j8 mdrun $ make install-mdrun the Warnings are of the form: gromacs-4.6-beta3/src/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h(80): warning #120: return value type does not match the function type return gmx_mm256_set_m128(t2,t1); gromacs-4.6-beta3/src/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h(204): warning #167: argument of type __m128d is incompatible with parameter of type __m128 t1 = gmx_mm256_set_m128(_mm_loadu_pd(p3),_mm_loadu_pd(p1)); /* c12c c6c | c12a c6a */ gromacs-4.6-beta3/src/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h(233): warning #556: a value of type __m256 cannot be assigned to an entity of type __m256d *x1 = gmx_mm256_set_m128(tx,tx); -- 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] specbond definition
Hi, In my system, I have a special bond (isopeptide bond, i.e., a bond between amino group of Lys and the carboxyl terminus of another protein). Before the simulation, is this bond should be formed or both LYS (which is defined with different residue name, e.g., LYX) and carboxyl terminus of another protein (which is Gly in my system; defined as GLX) should be in their standard forms (-NH3+, and -COO-, respectively). I defined this bond in specbond.dat as: LYX NZ 1 GLX C 1 0.135LYS2 GLY2 Serdar -- 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 on generate velocities and gen_temp in mdp files for REMD simulations
On 1/16/13 3:56 AM, Neha Gandhi wrote: Dear Help, I am trying to run REMD simulations and found couple of interesting discussions on GROMACS mailing list regarding ensembles which can be used during REMD. I will be running REMD of small peptide in explicit solvent and I am confused about gen_temp and gen_vel parameters for these simulations below: 1. NPT ensemble at 310 K to get density right. What should be the parameters gen_vel and gen_temp set to? That depends. If you do prior equilibration, like NVT, then you should not be re-generating velocities upon moving to NPT. If NPT is your first phase of equilibration, then gen_vel = yes and gen_temp is set to whatever the desired temperature is. The same is true for any equilibration protocol. 2. Equilibration at each temperature -NVT ensemble. Although equilibration run will be carried out for a reference temperature range, should the gen_temp still be set to 310K? If gen_vel = no, then the gen_temp setting is ignored. You should only ever initialize velocities once, at the start of whatever the first phase of equilibration is. Regenerating velocities later makes the previous equilibration pointless and may cause instabilities in your system. 3. Replica exchange -What should be gen_temp and gen_velocity set to? See point #2. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] specbond definition
On 1/16/13 6:54 AM, Serdar Durdagi, PhD wrote: Hi, In my system, I have a special bond (isopeptide bond, i.e., a bond between amino group of Lys and the carboxyl terminus of another protein). Before the simulation, is this bond should be formed or both LYS (which is defined with different residue name, e.g., LYX) and carboxyl terminus of another protein (which is Gly in my system; defined as GLX) should be in their standard forms (-NH3+, and -COO-, respectively). I defined this bond in specbond.dat as: LYX NZ 1 GLX C 1 0.135LYS2 GLY2 If the isopeptide bond should be present, it must be defined as such. Bonds won't break or form during MD, so if you have ionized groups and no bond, then none will ever emerge. You need to define the state you wish to simulate at the outset of the run. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Warning _mesage
On 1/16/13 5:32 AM, Devika N T wrote: 4.5.5 versio Writing topology Processing chain 2 'A' (4 atoms, 4 residues) Warning: Starting residue CA149 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA150 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA151 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA152 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. Note what the following line tells you: If this is incorrect, you can edit residuetypes.dat to modify the behavior. So pdb2gmx is recognizing CA (calcium?) as some unknown type. This may or may not be relevant for your purposes. The topology should have been written just fine as long as the parent force field recognizes CA. If it is an ion, do as pdb2gmx suggests and add this information to residuetypes.dat, which will make default group generation easier later on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Warning _mesage
Thank you Justin for your reply. I need to perform the effect of Calcium (CA) with protein Calmodulin. From the warning message its clear that CA is not identified as ion. But previously I tried the run with Gromacs version 4.0.7 at that time Version 4.0.7 Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' So I thought in version 4.5.5 it will have the residuetype.dat file updated with calcium. Fine let me try by adding calcium to residuetypes.dat Anyway I cannot consider calcium ion as ligand right? * Regards** N.T. Devika* On Wed, Jan 16, 2013 at 5:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/16/13 5:32 AM, Devika N T wrote: 4.5.5 versio Writing topology Processing chain 2 'A' (4 atoms, 4 residues) Warning: Starting residue CA149 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA150 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA151 in chain not identified as Protein/RNA/DNA. Warning: Starting residue CA152 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. Note what the following line tells you: If this is incorrect, you can edit residuetypes.dat to modify the behavior. So pdb2gmx is recognizing CA (calcium?) as some unknown type. This may or may not be relevant for your purposes. The topology should have been written just fine as long as the parent force field recognizes CA. If it is an ion, do as pdb2gmx suggests and add this information to residuetypes.dat, which will make default group generation easier later on. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- 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] Warning _mesage
On 1/16/13 7:38 AM, Devika N T wrote: Thank you Justin for your reply. I need to perform the effect of Calcium (CA) with protein Calmodulin. From the warning message its clear that CA is not identified as ion. But previously I tried the run with Gromacs version 4.0.7 at that time Version 4.0.7 Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' This only implies that the name is wrong with respect to what the .rtp file expects. So I thought in version 4.5.5 it will have the residuetype.dat file updated with calcium. Fine let me try by adding calcium to residuetypes.dat That should be the solution. Anyway I cannot consider calcium ion as ligand right? You can consider it however you like, but if you're interpreting a ligand to be something for which you need a topology from an external source, then no. All Gromacs force fields have parameters for calcium and should be processed automatically by pdb2gmx. In fact, I just checked residuetypes.dat and there is a line indicating CA as an Ion, so there should be no problem at all. Looking more closely at the pdb2gmx output from your original post, all that is indicating is that there is a species that is not Protein/DNA/RNA, which in this case is of course what one would expect. There is no problem whatsoever. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Warning _mesage
Thank you Justin for your valuable suggestion. I will follow it up. * Regards** N.T. Devika* On Wed, Jan 16, 2013 at 6:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/16/13 7:38 AM, Devika N T wrote: Thank you Justin for your reply. I need to perform the effect of Calcium (CA) with protein Calmodulin. From the warning message its clear that CA is not identified as ion. But previously I tried the run with Gromacs version 4.0.7 at that time Version 4.0.7 Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' Warning: 'CA' not found in residue topology database, trying to use 'CA2+' This only implies that the name is wrong with respect to what the .rtp file expects. So I thought in version 4.5.5 it will have the residuetype.dat file updated with calcium. Fine let me try by adding calcium to residuetypes.dat That should be the solution. Anyway I cannot consider calcium ion as ligand right? You can consider it however you like, but if you're interpreting a ligand to be something for which you need a topology from an external source, then no. All Gromacs force fields have parameters for calcium and should be processed automatically by pdb2gmx. In fact, I just checked residuetypes.dat and there is a line indicating CA as an Ion, so there should be no problem at all. Looking more closely at the pdb2gmx output from your original post, all that is indicating is that there is a species that is not Protein/DNA/RNA, which in this case is of course what one would expect. There is no problem whatsoever. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- 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-beta3 compile warnings intel-suite 2011 and 2013
Thanks, that's expected. We've fixed some issues here. Mark On Wed, Jan 16, 2013 at 12:22 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Hi Ronald, Using intel-suite/64/2013.0/079 with mkl with the release-4-6 branch version: f3dd8cb7ae23accff657551523d056**57262a72ff gave no compiler warnings for $ export CC=icc ; export CXX=icpc ; cmake -DGMX_MPI=OFF -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include -DMKL_LIBRARIES=$MKLROOT/lib/** intel64/libmkl_core.so;$**MKLROOT/lib/intel64/libmkl_** intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_sequential.so -DGMX_OPENMP=ON -DCMAKE_INSTALL_PREFIX=/home/**rb1109/libs/gromacs/bin ../ $ make -j8 mdrun $ make install-mdrun Thanks, Richard On 15/01/13 18:42, Roland Schulz wrote: Hi, could you check if you get these warnings also with the latest version from git? We have changed quite a bit sense then. git clone https://gerrit.gromacs.org/p/**gromacshttps://gerrit.gromacs.org/p/gromacs git checkout release-4-6 Roland On Tue, Jan 15, 2013 at 9:34 AM, Richard Broadbent richard.broadbent09@imperial.**ac.uk richard.broadben...@imperial.ac.uk wrote: Dear All, I've just installed 4.6-beta3 on my ubuntu linux (Intel Xeon [sandy bridge]) box using both intel-suite/64/2011.10/319, and intel-suite/64/2013.0/079 with mkl Using either compiler I received several hundred warnings of type #120, #167, and #556 (see bellow for examples). I thought this might be vaguely related to Bug #1074, as these all appear to be casting warnings. A small test md simulation ran as expected so the executable seems to be working and it is using AVX_256 acceleration. I therefore don't think this justifies a bug report but I did think it might be worth flagging up that these warnings occur and asking if other people had seen them. If anyone has any recommendations for how to get rid of them or thinks that they are significant I would also be interested. Thanks, Richard my cmake line was: $ export CC=icc ; export CXX=icpc ; cmake -DGMX_MPI=OFF -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include -DMKL_LIBRARIES=$MKLROOT/lib/**intel64/libmkl_core.so;$** MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/** intel64/libmkl_sequential.so -DGMX_OPENMP=ON ../ and I then built it with: $ make -j8 mdrun $ make install-mdrun the Warnings are of the form: gromacs-4.6-beta3/src/gmxlib/**nonbonded/nb_kernel_avx_256_** double/kernelutil_x86_avx_256_**double.h(80): warning #120: return value type does not match the function type return gmx_mm256_set_m128(t2,t1); gromacs-4.6-beta3/src/gmxlib/**nonbonded/nb_kernel_avx_256_** double/kernelutil_x86_avx_256_**double.h(204): warning #167: argument of type __m128d is incompatible with parameter of type __m128 t1 = gmx_mm256_set_m128(_mm_loadu_**pd(p3),_mm_loadu_pd(p1)); /* c12c c6c | c12a c6a */ gromacs-4.6-beta3/src/gmxlib/**nonbonded/nb_kernel_avx_256_** double/kernelutil_x86_avx_256_**double.h(233): warning #556: a value of type __m256 cannot be assigned to an entity of type __m256d *x1 = gmx_mm256_set_m128(tx,tx); -- 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 -- 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 -- 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] meta-dynamics in gromacs-4.6
The GROMACS team has no plans for that. The usual problem here is that everybody would like every algorithm included, but that developers with time and experience are scarce :-) It's an open source project though, so anyone can do whatever they like. We're prepared to consider inclusions to the main project. Note that we're doing a major rework of the code base to C++ in the next year (or more), so people implementing new features may wish to consider that in their choice to write code :-) Mark On Tue, Jan 15, 2013 at 2:26 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs developers! There is well-known plugin plumed which can be used for implementation of meta-dynamics simulation if Gromacs-4.5. I wounder to know if it possible to include some meta-dynamics options in the new gromacs release ( similar to inclusion of essential dynamics sampling in previous gromacs versions) ? Thanks for attention, 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] 60% slowdown with GPU / verlet and sd integrator
Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check1244.988096 11204.893 0.1 NxN QSTab Elec. + VdW [F] 194846.615488 7988711.23591.9 NxN QSTab Elec. + VdW [VF] 2009.923008 118585.457 1.4 1,4 nonbonded interactions 31.6163222845.469 0.0 Calc Weights 703.010574 25308.381 0.3 Spread Q Bspline 14997.558912 29995.118 0.3 Gather F Bspline 14997.558912 89985.353 1.0 3D-FFT 47658.567884 381268.543 4.4 Solve PME 20.5808961317.177 0.0 Shift-X 9.418458 56.511 0.0 Angles 21.8793753675.735 0.0 Propers 48.599718 11129.335 0.1 Virial 23.498403 422.971 0.0 Stop-CM 2.436616 24.366 0.0 Calc-Ekin 93.8097162532.862 0.0 Lincs 12.147284 728.837 0.0 Lincs-Mat 131.328750 525.315 0.0 Constraint-V 246.6336141973.069 0.0 Constraint-Vir 23.486379 563.673 0.0 Settle 74.129451 23943.813 0.3 - Total 8694798.114 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search18201 0.944 27.206 3.3 Launch GPU ops.18 5001 0.371 10.690 1.3 Force 18 5001 2.185 62.987 7.7 PME mesh 18 5001 15.033 433.44152.9 Wait GPU local 18 5001 1.551 44.719 5.5 NB X/F buffer ops. 18 9801 0.538 15.499 1.9 Write traj.18 2 0.725 20.912 2.6 Update 18 5001 2.318 66.826 8.2 Constraints18 5001 2.898 83.55110.2 Rest 1 1.832 52.828 6.5 - Total 1 28.394 818.659 100.0 - -
RE: [gmx-users] 60% slowdown with GPU / verlet and sd integrator
Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk Date: Wed, 16 Jan 2013 17:26:18 +0300 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check 1244.988096 11204.893 0.1 NxN QSTab Elec. + VdW [F] 194846.615488 7988711.235 91.9 NxN QSTab Elec. + VdW [VF] 2009.923008 118585.457 1.4 1,4 nonbonded interactions 31.616322 2845.469 0.0 Calc Weights 703.010574 25308.381 0.3 Spread Q Bspline 14997.558912 29995.118 0.3 Gather F Bspline 14997.558912 89985.353 1.0 3D-FFT 47658.567884 381268.543 4.4 Solve PME 20.580896 1317.177 0.0 Shift-X 9.418458 56.511 0.0 Angles 21.879375 3675.735 0.0 Propers 48.599718 11129.335 0.1 Virial 23.498403 422.971 0.0 Stop-CM 2.436616 24.366 0.0 Calc-Ekin 93.809716 2532.862 0.0 Lincs 12.147284 728.837 0.0 Lincs-Mat 131.328750 525.315 0.0 Constraint-V 246.633614 1973.069 0.0 Constraint-Vir 23.486379 563.673 0.0 Settle 74.129451 23943.813 0.3 - Total 8694798.114 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search 1 8 201 0.944 27.206 3.3 Launch GPU ops. 1 8 5001 0.371 10.690 1.3 Force 1 8 5001 2.185 62.987 7.7 PME mesh 1 8 5001 15.033 433.441 52.9 Wait GPU local 1 8 5001 1.551 44.719 5.5 NB X/F buffer ops. 1 8 9801 0.538 15.499 1.9 Write traj. 1 8 2 0.725 20.912 2.6 Update 1 8 5001 2.318 66.826 8.2 Constraints 1 8 5001 2.898 83.551 10.2 Rest 1 1.832 52.828 6.5 - Total 1 28.394 818.659 100.0 - - PME spread/gather 1 8 10002 8.745 252.144 30.8 PME 3D-FFT 1 8 10002 5.392 155.458 19.0 PME solve 1 8 5001 0.869 25.069 3.1 - GPU timings - Computing: Count Wall t (s) ms/step % - Pair list H2D 201 0.080 0.397 0.4 X / q H2D 5001 0.698 0.140 3.7 Nonbonded F kernel 4400 14.856 3.376 79.1 Nonbonded F+ene k. 400 1.667 4.167 8.9 Nonbonded F+prune k. 100 0.441 4.407 2.3
[gmx-users] how to convert a dodecahedric trajectory into a triclinic one?
Dear All, I performed a MD simulation of a protein into a rhombic dodecahedric box. Now I'd need to convert this dodecahedric box into a triclinic one (I mean, not only for one frame to obtain a .gro file, but for the entire trajectory). I think that it would be possible using trjconv command, but I have some trouble in doing it, I don't understand which are the correct flags to use. Could anybody give me some suggestion about this problem? Many thanks in advance and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] 60% slowdown with GPU / verlet and sd integrator
We should probably note this effect on the wiki somewhere? Mark On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess g...@hotmail.com wrote: Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk Date: Wed, 16 Jan 2013 17:26:18 +0300 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check 1244.988096 11204.893 0.1 NxN QSTab Elec. + VdW [F] 194846.615488 7988711.235 91.9 NxN QSTab Elec. + VdW [VF] 2009.923008 118585.457 1.4 1,4 nonbonded interactions 31.616322 2845.469 0.0 Calc Weights 703.010574 25308.381 0.3 Spread Q Bspline 14997.558912 29995.118 0.3 Gather F Bspline 14997.558912 89985.353 1.0 3D-FFT 47658.567884 381268.543 4.4 Solve PME 20.580896 1317.177 0.0 Shift-X 9.418458 56.511 0.0 Angles 21.879375 3675.735 0.0 Propers 48.599718 11129.335 0.1 Virial 23.498403 422.971 0.0 Stop-CM 2.436616 24.366 0.0 Calc-Ekin 93.809716 2532.862 0.0 Lincs 12.147284 728.837 0.0 Lincs-Mat 131.328750 525.315 0.0 Constraint-V 246.633614 1973.069 0.0 Constraint-Vir 23.486379 563.673 0.0 Settle 74.129451 23943.813 0.3 - Total 8694798.114 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search 1 8 201 0.944 27.206 3.3 Launch GPU ops. 1 8 5001 0.371 10.690 1.3 Force 1 8 5001 2.185 62.987 7.7 PME mesh 1 8 5001 15.033 433.441 52.9 Wait GPU local 1 8 5001 1.551 44.719 5.5 NB X/F buffer ops. 1 8 9801 0.538 15.499 1.9 Write traj. 1 8 2 0.725 20.912 2.6 Update 1 8 5001 2.318 66.826 8.2 Constraints 1 8 5001 2.898 83.551 10.2 Rest 1 1.832 52.828 6.5 - Total 1 28.394 818.659 100.0 - - PME spread/gather 1 8 10002 8.745 252.144 30.8 PME 3D-FFT 1 8 10002 5.392 155.458 19.0 PME solve 1 8 5001 0.869 25.069 3.1 - GPU timings - Computing: Count Wall t (s)
Re: [gmx-users] how to convert a dodecahedric trajectory into a triclinic one?
On 2013-01-16 16:03, Anna Marabotti wrote: Dear All, I performed a MD simulation of a protein into a rhombic dodecahedric box. Now I'd need to convert this dodecahedric box into a triclinic one (I mean, not only for one frame to obtain a .gro file, but for the entire trajectory). I think that it would be possible using trjconv command, but I have some trouble in doing it, I don't understand which are the correct flags to use. Could anybody give me some suggestion about this problem? Many thanks in advance and best regards Anna It already is a triclinic box. You don't have to do anything. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] 60% slowdown with GPU / verlet and sd integrator
The issue I'm referring to is about a factor of 2 in update and constraints, but here it's much more. I just found out that the SD update is not OpenMP threaded (and I even noted in the code why this is). I reopened the issue and will find a solution. Cheers. Berk Date: Wed, 16 Jan 2013 16:20:32 +0100 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: mark.j.abra...@gmail.com To: gmx-users@gromacs.org We should probably note this effect on the wiki somewhere? Mark On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess g...@hotmail.com wrote: Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk Date: Wed, 16 Jan 2013 17:26:18 +0300 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check 1244.988096 11204.893 0.1 NxN QSTab Elec. + VdW [F] 194846.615488 7988711.235 91.9 NxN QSTab Elec. + VdW [VF] 2009.923008 118585.457 1.4 1,4 nonbonded interactions 31.616322 2845.469 0.0 Calc Weights 703.010574 25308.381 0.3 Spread Q Bspline 14997.558912 29995.118 0.3 Gather F Bspline 14997.558912 89985.353 1.0 3D-FFT 47658.567884 381268.543 4.4 Solve PME 20.580896 1317.177 0.0 Shift-X 9.418458 56.511 0.0 Angles 21.879375 3675.735 0.0 Propers 48.599718 11129.335 0.1 Virial 23.498403 422.971 0.0 Stop-CM 2.436616 24.366 0.0 Calc-Ekin 93.809716 2532.862 0.0 Lincs 12.147284 728.837 0.0 Lincs-Mat 131.328750 525.315 0.0 Constraint-V 246.633614 1973.069 0.0 Constraint-Vir 23.486379 563.673 0.0 Settle 74.129451 23943.813 0.3 - Total 8694798.114 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search 1 8 201 0.944 27.206 3.3 Launch GPU ops. 1 8 5001 0.371 10.690 1.3 Force 1 8 5001 2.185 62.987 7.7 PME mesh 1 8 5001 15.033 433.441 52.9 Wait GPU local 1 8 5001 1.551 44.719 5.5 NB X/F buffer ops. 1 8 9801 0.538 15.499 1.9 Write traj. 1 8 2 0.725 20.912 2.6 Update 1 8 5001 2.318 66.826 8.2 Constraints 1 8 5001 2.898 83.551 10.2 Rest 1 1.832 52.828 6.5
[gmx-users] RE: No default Proper Dih. types
Hello all, I have the same problem, but I think the dihedral is properly defined. I am running a polymer with the G53A6 force field. First I use pdb2gmx to generate a conf and a top file. When I run grompp, I have the error(s): ERROR 1 [file topol.top, line 1507]: No default Proper Dih. types Then I go to the topol.top file, line 1507, which contains, inside the [ dihedrals ] directive: 1 21011 1 It is clear that it does not have a torsion type defined for this atoms. I look at the beginning of the same top file, to know of what type are atoms 1, 2, 10, and 11, and in what residue they are: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1CH3 1MEA CB 1 0 15.035 ; qtot 0 2CH1 2NIPCA1 2 0 13.019 ; qtot 0 3 C 2NIP C 3 0.45 12.011 ; qtot 0.45 4 O 2NIP O 3 -0.4515.9994 ; qtot 0 5 N 2NIP N 4 -0.3114.0067 ; qtot -0.31 6 H 2NIP H 4 0.31 1.008 ; qtot 0 7CH1 2NIPCA2 5 0 13.019 ; qtot 0 8CH3 2NIPCB1 5 0 15.035 ; qtot 0 9CH3 2NIPCB2 5 0 15.035 ; qtot 0 10CH2 3MEM CB 6 0 14.027 ; qtot 0 11CH1 4NIPCA1 7 0 13.019 ; qtot 0 ...etc Now I look to my aminoacids.rtp file. There I have the residues defined: [ MEA ] [ atoms ] CB CH3 0.0001 [ bonds ] [ MEM ] [ atoms ] CB CH2 0.0001 [ bonds ] CB -CA1 gb_27 [ angles ] CB -CA1 -CB ga_15 [ MEE ] [ atoms ] CB CH3 0.0001 [ bonds ] CB -CA1 gb_27 [ angles ] -CB -CA1 CB ga_15 [ NIP ] [ atoms ] CA1CH1 0.000 1 C C 0.450 2 O O -0.450 2 N N -0.310 3 H H 0.310 3 CA2CH1 0.000 4 CB1CH3 0.000 4 CB2CH3 0.000 4 [ bonds ] CA1 C gb_27 CO gb_5 CN gb_11 NH gb_2 NCA2 gb_21 CA2 CB1 gb_27 CA2 CB2 gb_27 CA1 -CB gb_27 [ angles ] -CB CA1 +CB ga_15 -CB CA1 Cga_13 C CA1 +CB ga_13 CA1 COga_30 CA1 CNga_19 OCNga_33 CNHga_32 CNCA2 ga_31 HNCA2 ga_18 NCA2 CB1 ga_13 NCA2 CB2 ga_13 CB1 CA2 CB2 ga_15 CA1 +CB +CA1 ga_15 [ dihedrals ] -CB CA1 +CB +CA1 gd_34 -CB CA1 CNgd_40 CA1 CNCA2 gd_14 CNCA2 CB1 gd_39 CA1 +CB +CA1 +Cgd_34 [ impropers ] CA1 -CB +CB Cgi_2 CCA1 NOgi_1 NCCA2 Hgi_1 CA2 NCB1 CB2 gi_2 As I understand it, the torsion grompp is complaining about is the first torsion defined in the NIP residue. I have tried, just in case, to write that torsion in different ways, at a different order, in the residue MEM, changing atom names to the name they have in atomtypes.atp... but without success. Any idea what happens? Kind regards -- View this message in context: http://gromacs.5086.n6.nabble.com/No-default-Proper-Dih-types-tp4442749p5004621.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
Re: [gmx-users] RE: No default Proper Dih. types
On 1/16/13 10:58 AM, escajarro wrote: Hello all, I have the same problem, but I think the dihedral is properly defined. I am running a polymer with the G53A6 force field. First I use pdb2gmx to generate a conf and a top file. When I run grompp, I have the error(s): ERROR 1 [file topol.top, line 1507]: No default Proper Dih. types Then I go to the topol.top file, line 1507, which contains, inside the [ dihedrals ] directive: 1 21011 1 It is clear that it does not have a torsion type defined for this atoms. I look at the beginning of the same top file, to know of what type are atoms 1, 2, 10, and 11, and in what residue they are: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1CH3 1MEA CB 1 0 15.035 ; qtot 0 2CH1 2NIPCA1 2 0 13.019 ; qtot 0 3 C 2NIP C 3 0.45 12.011 ; qtot 0.45 4 O 2NIP O 3 -0.4515.9994 ; qtot 0 5 N 2NIP N 4 -0.3114.0067 ; qtot -0.31 6 H 2NIP H 4 0.31 1.008 ; qtot 0 7CH1 2NIPCA2 5 0 13.019 ; qtot 0 8CH3 2NIPCB1 5 0 15.035 ; qtot 0 9CH3 2NIPCB2 5 0 15.035 ; qtot 0 10CH2 3MEM CB 6 0 14.027 ; qtot 0 11CH1 4NIPCA1 7 0 13.019 ; qtot 0 ...etc Now I look to my aminoacids.rtp file. There I have the residues defined: [ MEA ] [ atoms ] CB CH3 0.0001 [ bonds ] [ MEM ] [ atoms ] CB CH2 0.0001 [ bonds ] CB -CA1 gb_27 [ angles ] CB -CA1 -CB ga_15 [ MEE ] [ atoms ] CB CH3 0.0001 [ bonds ] CB -CA1 gb_27 [ angles ] -CB -CA1 CB ga_15 [ NIP ] [ atoms ] CA1CH1 0.000 1 C C 0.450 2 O O -0.450 2 N N -0.310 3 H H 0.310 3 CA2CH1 0.000 4 CB1CH3 0.000 4 CB2CH3 0.000 4 [ bonds ] CA1 C gb_27 CO gb_5 CN gb_11 NH gb_2 NCA2 gb_21 CA2 CB1 gb_27 CA2 CB2 gb_27 CA1 -CB gb_27 [ angles ] -CB CA1 +CB ga_15 -CB CA1 Cga_13 C CA1 +CB ga_13 CA1 COga_30 CA1 CNga_19 OCNga_33 CNHga_32 CNCA2 ga_31 HNCA2 ga_18 NCA2 CB1 ga_13 NCA2 CB2 ga_13 CB1 CA2 CB2 ga_15 CA1 +CB +CA1 ga_15 [ dihedrals ] -CB CA1 +CB +CA1 gd_34 -CB CA1 CNgd_40 CA1 CNCA2 gd_14 CNCA2 CB1 gd_39 CA1 +CB +CA1 +Cgd_34 [ impropers ] CA1 -CB +CB Cgi_2 CCA1 NOgi_1 NCCA2 Hgi_1 CA2 NCB1 CB2 gi_2 As I understand it, the torsion grompp is complaining about is the first torsion defined in the NIP residue. I have tried, just in case, to write that torsion in different ways, at a different order, in the residue MEM, changing atom names to the name they have in atomtypes.atp... but without success. Any idea what happens? Atom names and .rtp files are largely irrelevant here. You have a torsion specified with atom types CH3-CH1-CH2-CH1. If there are no parameters in ffbonded.itp for that interaction, grompp is going to give you that error message. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] merge many boxes
On 1/16/13 10:09 AM, Kieu Thu Nguyen wrote: Dear All, I want to merge two or many boxes with the same size into one new box. The size of new box is not a multiples of old box size. And the molecules that overlap have to be removed. In Gromacs, are there any tool for my problem ? See the logic of constructing heterogeneous systems here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html You can position one component anywhere in a unit cell with editconf -center, and potentially fill the other half with a solvent using genbox -cs, which will remove overlapping molecules, but any system more complex than stacking a few boxes in the same dimension will not be very easy. With the editconf -center method, one could conceivably place any number of boxes anywhere in the unit cell, but there is no automatic removal of overlapping atoms. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization problem
On Wed, Jan 16, 2013 at 8:37 AM, Marcelo Depolo marcelodep...@gmail.com wrote: I was minimizing my system (with only proteins) and i got this error in the log: *Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-01 Number of steps= -1 F-max = 4.76837e+04 on atom 3684 F-Norm= 2.99917e+02 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.1 WARNING: there may be something wrong with energy file prt_cg.edr Found: step=-1, nre=36, nblock=0, time=-1. Trying to skip frame expect a crash though* http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- 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] Rerun trajectory does not contain a box
Dear gmx users, Background: I just finished my 100 ns md simulation on a receptor in membrane and I got all my .trr .xtc and .edr output files In order to calculate the energy potential only for the protein, I made a new .mdp defining energygrps : Protein, thus obtaining a new .tpr for a rerun with mdrun. The problem is that, if I use the trajectory file 100ns.trr , the following error message comes out: Source code file: md.c, line: 626 Fatal error: Rerun trajectory frame step 5000 time 10.00 does not contain a box, while pbc is used For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On the contrary if I use the trajectory file 100ns.xtc the calculation proceeds with no errors. I think gromacs reads the box xyz from the coordinate file. I also know that is better to use the .trr file while rerunnig a calculation, so what do you think could be wrong? Thank you for your kind help Luca -- 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] merge many boxes
You should try packmol software. You will need to use a pdb formats, but then you transform to .gro with pdb2gmx. It´s free and very easy to use. http://www.ime.unicamp.br/~martinez/packmol/ Flor Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junín 956 6º (1113) TE: 54 011 4964-8273 De: Kieu Thu Nguyen kieuthu2...@gmail.com Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviado: miércoles, 16 de enero de 2013 13:09 Asunto: [gmx-users] merge many boxes Dear All, I want to merge two or many boxes with the same size into one new box. The size of new box is not a multiples of old box size. And the molecules that overlap have to be removed. In Gromacs, are there any tool for my problem ? Thanks in advance ! Regards, KT -- 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
Re: [gmx-users] Minimization problem
Thanks, Elton. I appreciate your answer, but my question was about the Warning error. The convergence value was set ok. The minimization do not go further because the error: *WARNING: there may be something wrong with energy file prt_cg.edr Found: step=-1, nre=36, nblock=0, time=-1. Trying to skip frame expect a crash though* Anyone knows about this particular error message? Thanks! -- Marcelo Depólo Polêto Molecular Animal Infectology Laboratory - LIMA Department of Biochemistry and Molecular Biology Universidade Federal de Viçosa - UFV - Brazil -- 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] Minimization problem
On Wed, Jan 16, 2013 at 3:11 PM, Marcelo Depolo marcelodep...@gmail.com wrote: Thanks, Elton. I appreciate your answer, but my question was about the Warning error. The convergence value was set ok. The minimization do not go further because the error: *WARNING: there may be something wrong with energy file prt_cg.edr Found: step=-1, nre=36, nblock=0, time=-1. Trying to skip frame expect a crash though* Anyone knows about this particular error message? Thanks! Sorry, I missed that part. The minimization really stops because of the small stepsize. The warning you mentioned is probably not directly related to mdrun stopping. What's your nstenergy value set in the mdp file? -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- 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] Minimization problem
On 1/16/13 12:11 PM, Marcelo Depolo wrote: Thanks, Elton. I appreciate your answer, but my question was about the Warning error. The convergence value was set ok. The minimization do not go further because the error: *WARNING: there may be something wrong with energy file prt_cg.edr Found: step=-1, nre=36, nblock=0, time=-1. Trying to skip frame expect a crash though* Anyone knows about this particular error message? What version of Gromacs are you using? What does gmxcheck tell you about the .edr file? Is the problem reproducible, or did it happen just once? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization problem
I have set nstenergy=100. I'm using gromacs compiled with double precision and even so, the stepsize was too small. i have faced this convergence problems earlier, and managed some solutions. I'm really wondering about the warning part, that I have never seen. -- Marcelo Depólo Polêto -- 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] Minimization problem
Justin, I'm using gromacs 4.5.5 version, compiled in double precision. I tried to generate the .tpr file 3 times and got the same results. About the gmxcheck, i don't know how to use it to check my .edr file. How can I do this? -- Marcelo Depólo Polêto -- 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] meta-dynamics in gromacs-4.6
I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED developers use Gromacs. Perhaps any PLUMED lurkers on the list can speak up. . . . On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham mark.j.abra...@gmail.com wrote: The GROMACS team has no plans for that. The usual problem here is that everybody would like every algorithm included, but that developers with time and experience are scarce :-) It's an open source project though, so anyone can do whatever they like. We're prepared to consider inclusions to the main project. Note that we're doing a major rework of the code base to C++ in the next year (or more), so people implementing new features may wish to consider that in their choice to write code :-) Mark On Tue, Jan 15, 2013 at 2:26 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs developers! There is well-known plugin plumed which can be used for implementation of meta-dynamics simulation if Gromacs-4.5. I wounder to know if it possible to include some meta-dynamics options in the new gromacs release ( similar to inclusion of essential dynamics sampling in previous gromacs versions) ? Thanks for attention, 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] Minimization problem
On 1/16/13 12:36 PM, Marcelo Depolo wrote: Justin, I'm using gromacs 4.5.5 version, compiled in double precision. I tried to generate the .tpr file 3 times and got the same results. About the gmxcheck, i don't know how to use it to check my .edr file. How can I do this? Start with reading gmxcheck -h :) The -e flag reads in a .edr file and checks its integrity. If you can verify that this problem still persists with version 4.6beta3, then it may be worth a bug report to see what's going on. Seems like there's an I/O issue. Does it only affect double precision or single as well? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] merge many boxes
Thank Justin and Flor so much ! Sorry about my unclear question. I mean that my boxes is not isotropic. Each box has many types of molecules such as water, lipid, ... Are those tools that you adviced me available for this problem ? Regards, KT On Wed, Jan 16, 2013 at 11:46 PM, FLOR MARTINI flormart...@yahoo.com.arwrote: You should try packmol software. You will need to use a pdb formats, but then you transform to .gro with pdb2gmx. It´s free and very easy to use. http://www.ime.unicamp.br/~martinez/packmol/ Flor Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junín 956 6º (1113) TE: 54 011 4964-8273 De: Kieu Thu Nguyen kieuthu2...@gmail.com Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviado: miércoles, 16 de enero de 2013 13:09 Asunto: [gmx-users] merge many boxes Dear All, I want to merge two or many boxes with the same size into one new box. The size of new box is not a multiples of old box size. And the molecules that overlap have to be removed. In Gromacs, are there any tool for my problem ? Thanks in advance ! Regards, KT -- 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] Re: meta-dynamics in gromacs-4.6
Hi, yes I can confirm you that PLUMED will be available for gromacs-4.6! We are currently testing it. Carlo Message: 6 Date: Wed, 16 Jan 2013 12:54:11 -0500 From: Michael Shirts mrshi...@gmail.com Subject: Re: [gmx-users] meta-dynamics in gromacs-4.6 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CA+zJb=huGQ=3xnhcosfqwsx1mbkmadu8bd9u2t7loojvn7a...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED developers use Gromacs. Perhaps any PLUMED lurkers on the list can speak up. . . . On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham mark.j.abra...@gmail.com wrote: The GROMACS team has no plans for that. The usual problem here is that everybody would like every algorithm included, but that developers with time and experience are scarce :-) It's an open source project though, so anyone can do whatever they like. We're prepared to consider inclusions to the main project. Note that we're doing a major rework of the code base to C++ in the next year (or more), so people implementing new features may wish to consider that in their choice to write code :-) Mark On Tue, Jan 15, 2013 at 2:26 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs developers! There is well-known plugin plumed which can be used for implementation of meta-dynamics simulation if Gromacs-4.5. I wounder to know if it possible to include some meta-dynamics options in the new gromacs release ( similar to inclusion of essential dynamics sampling in previous gromacs versions) ? Thanks for attention, 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] merge many boxes
On 1/16/13 4:39 PM, Kieu Thu Nguyen wrote: Thank Justin and Flor so much ! Sorry about my unclear question. I mean that my boxes is not isotropic. Each box has many types of molecules such as water, lipid, ... Are those tools that you adviced me available for this problem ? That depends on what you're trying to do. It is still not clear to me what you want to assemble. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] merge many boxes
@Justin, i am trying to simulate oligomerization of membrane protein. I want to assemble a big box with proteins from many small box having a protein. Is it available ? @Flor, thanks you so much for your advice. I will try, i hope it helpful :-) On Thu, Jan 17, 2013 at 5:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/16/13 4:39 PM, Kieu Thu Nguyen wrote: Thank Justin and Flor so much ! Sorry about my unclear question. I mean that my boxes is not isotropic. Each box has many types of molecules such as water, lipid, ... Are those tools that you adviced me available for this problem ? That depends on what you're trying to do. It is still not clear to me what you want to assemble. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- 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] merge many boxes
On 1/16/13 8:26 PM, Kieu Thu Nguyen wrote: @Justin, i am trying to simulate oligomerization of membrane protein. I want to assemble a big box with proteins from many small box having a protein. Is it available ? The method I described previously should work. You place one patch (membrane + embedded protein) at some location within a large box using editconf -center, then combine with any other system(s) that have similarly been positioned using editconf -center. The tutorial I linked before demonstrates a trivial example of something similar, but it illustrates the logic behind the process. You won't get any clashes to be automatically resolved/molecules deleted, but even with small gaps or unequilibrated boundaries, a gentle equilibration protocol should resolve those issues. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Removing external bias apart from umbrella potential
Hi, I am recently trying to perform an umbrella sampling simulation along a particular reaction coordinate on a system where I have also put position restraint on certain atoms of the system... So, for each umbrella sampling window, I have an extra potential on certain atoms ( due to the position restraint ) apart from the umbrella potential. I am using Gromacs4.5.4 for the simulation. So, after carrying out the umbrella sampling simulation, if I use WHAM to remove the bias, I think WHAM, in its present implementation, can only remove the bias due to the umbrella potential. But the bias required for position-restraining certain atoms remains still there in the computed PMF. So, I was wondering whether you can suggest any way-out for removing that bias from the PMF due to position restraints as well. Sanku -- 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] DD cells - regd
Dear Bogdan Costescu, Thank you for your valuable suggestion. Regards, Ramesh. On Mon, Jan 14, 2013 at 8:20 PM, Bogdan Costescu bcoste...@gmail.comwrote: On Sat, Jan 12, 2013 at 10:04 AM, ramesh cheerla rameshgrom...@gmail.com wrote: This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells This gives another possible solution. You decrease the number of DD grid cells by reducing the numbers of cores on which mdrun runs. Or, for the same number of cores, you can control better the decomposition using the '-dd' option in case the constraints are aligned to one of the 3 main directions. Cheers, Bogdan -- 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] 60% slowdown with GPU / verlet and sd integrator
Hi, Just to note for the users who might read this: the report is valid, some non-thread-parallel code is the reason and we hope to have a fix for 4.6.0. For updates, follow the issue #1211. Cheers, -- Szilárd On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess g...@hotmail.com wrote: The issue I'm referring to is about a factor of 2 in update and constraints, but here it's much more. I just found out that the SD update is not OpenMP threaded (and I even noted in the code why this is). I reopened the issue and will find a solution. Cheers. Berk Date: Wed, 16 Jan 2013 16:20:32 +0100 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: mark.j.abra...@gmail.com To: gmx-users@gromacs.org We should probably note this effect on the wiki somewhere? Mark On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess g...@hotmail.com wrote: Hi, Unfortunately this is not a bug, but a feature! We made the non-bondeds so fast on the GPU that integration and constraints take more time. The sd1 integrator is almost as fast as the md integrator, but slightly less accurate. In most cases that's a good solution. I closed the redmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk Date: Wed, 16 Jan 2013 17:26:18 +0300 Subject: Re: [gmx-users] 60% slowdown with GPU / verlet and sd integrator From: jmsstarli...@gmail.com To: gmx-users@gromacs.org Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Páll szilard.p...@cbr.su.se: Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote: Hi, I'm seeing MD simulation running a lot slower with the sd integrator than with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented indication that this should be the case. Timings and logs pasted in below - wall time seems to be accumulating up in Update and Rest, adding up to 60% of total. The effect is still there without GPU, ca. 40% slowdown when switching from group to Verlet with the SD integrator System: Xeon E5-1620, 1x GTX 680, gromacs 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0 I didn't file a bug report yet as I don't have much variety of testing conditions available right now, I hope someone else has a moment to try to reproduce? Timings: cpu (ns/day) sd / verlet: 6 sd / group: 10 md / verlet: 9.2 md / group: 11.4 gpu (ns/day) sd / verlet: 11 md / verlet: 29.8 **MD integrator, GPU / verlet M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check 1244.988096 11204.893 0.1 NxN QSTab Elec. + VdW [F] 194846.615488 7988711.235 91.9 NxN QSTab Elec. + VdW [VF] 2009.923008 118585.457 1.4 1,4 nonbonded interactions 31.616322 2845.469 0.0 Calc Weights 703.010574 25308.381 0.3 Spread Q Bspline 14997.558912 29995.118 0.3 Gather F Bspline 14997.558912 89985.353 1.0 3D-FFT 47658.567884 381268.543 4.4 Solve PME 20.580896 1317.177 0.0 Shift-X 9.418458 56.511 0.0 Angles 21.879375 3675.735 0.0 Propers 48.599718 11129.335 0.1 Virial 23.498403 422.971 0.0 Stop-CM 2.436616 24.366 0.0 Calc-Ekin 93.809716 2532.862 0.0 Lincs 12.147284 728.837 0.0 Lincs-Mat 131.328750 525.315 0.0 Constraint-V 246.633614 1973.069 0.0 Constraint-Vir 23.486379 563.673 0.0 Settle 74.129451 23943.813 0.3 - Total 8694798.114 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles %
Re: [gmx-users] Re: meta-dynamics in gromacs-4.6
Thank you! It's a good news! James 2013/1/17 Carlo Camilloni carlo.camill...@gmail.com: Hi, yes I can confirm you that PLUMED will be available for gromacs-4.6! We are currently testing it. Carlo Message: 6 Date: Wed, 16 Jan 2013 12:54:11 -0500 From: Michael Shirts mrshi...@gmail.com Subject: Re: [gmx-users] meta-dynamics in gromacs-4.6 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CA+zJb=huGQ=3xnhcosfqwsx1mbkmadu8bd9u2t7loojvn7a...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED developers use Gromacs. Perhaps any PLUMED lurkers on the list can speak up. . . . On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham mark.j.abra...@gmail.com wrote: The GROMACS team has no plans for that. The usual problem here is that everybody would like every algorithm included, but that developers with time and experience are scarce :-) It's an open source project though, so anyone can do whatever they like. We're prepared to consider inclusions to the main project. Note that we're doing a major rework of the code base to C++ in the next year (or more), so people implementing new features may wish to consider that in their choice to write code :-) Mark On Tue, Jan 15, 2013 at 2:26 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs developers! There is well-known plugin plumed which can be used for implementation of meta-dynamics simulation if Gromacs-4.5. I wounder to know if it possible to include some meta-dynamics options in the new gromacs release ( similar to inclusion of essential dynamics sampling in previous gromacs versions) ? Thanks for attention, 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 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] residuetype.dat file missing
It should be in the top folder. If you install GROMACS recently and can not find the .dat just install GROMACS again. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Devika N T Sent: Thursday, 17 January 2013 4:34 PM To: Discussion list for GROMACS users Subject: [gmx-users] residuetype.dat file missing Hi all I Could not figure out any file by name residuetypes.dat I have seen in the usr/share/gromacs/top folder. I am using gromacs version 4.5.5. Is it some installation problem? * Regards** N.T. Devika* -- 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] residuetype.dat file missing
Thank you Emanuel I have followed the path only usr/share/gromacs/top -- but was missing Then I followed /usr/local/gromacs/share/gromacs/top - I could find residuetype.dat Previously I was having gromacs version 4.0.7, now I have installed 4.5.5. So I doubt some problem which removing and installing... * Regards** N.T. Devika* On Thu, Jan 17, 2013 at 11:36 AM, Emanuel Birru emanuel.bi...@monash.eduwrote: It should be in the top folder. If you install GROMACS recently and can not find the .dat just install GROMACS again. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Devika N T Sent: Thursday, 17 January 2013 4:34 PM To: Discussion list for GROMACS users Subject: [gmx-users] residuetype.dat file missing Hi all I Could not figure out any file by name residuetypes.dat I have seen in the usr/share/gromacs/top folder. I am using gromacs version 4.5.5. Is it some installation problem? * Regards** N.T. Devika* -- 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
