[gmx-users] Error using double precision
I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 4 out of 8 --- Program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]), VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1335. It should have been within [ 0 .. 1296 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Thanx for Using GROMACS - Have a Nice Day Error on node 6, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 6 out of 8 gcq#10922: Thanx for Using GROMACS - Have a Nice Day * MPI-error in rank 2 Routine MPI_Abort : Terminating after call to MPI_Abort * --- mpimon --- Aborting run after process-2 terminated abnormally Childprocess 17353 exited with exitcode 2 --- gcq#10922: Thanx for Using GROMACS - Have a Nice Day Thankful for some help. Edvin --- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebro, Sweden Tel: +46 19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code methods?
I'm no umbrella user, but as far as I know, you have to set different parameters, according to the manual. These may be similar to the AFM parameters, but still, in the config file, they are separated. Sure, you don't define a pull rate for Umbrella, because you build, as you said, discrete systems, where you put the umbrella potential onto one group along a reaction coordinate. It's clear that, depending on your system, you have to build N systems where your ligand is moved away from the protein along the reaction coordinate. Now, I'm curious about you asking about afm_init again...so you are finished with the umbrella business and want to do AFM now? The sentence, in fact, is very clear. You can break down the statement to: Calculate the resulting vector from the difference of two other vectors Therefore you have to find two vectors. One should be the COM of your reference group (you could also choose a single atom there...Just makes no sense to me) and one is either the COM of your ligand or, better, one single atom of your ligand, where the spring(AFM-tip) is attached to... I think, this has been discussed in the mailing list more than once... Maybe you should intensively search the archive for such things... regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete simulations. i.e. 21 simulation windows. I kind of get the idea that you will have to manually set up the the 21 discrete simulations to get the final separated ligand-protein for the umberalla method? correct me if I am wrong. The other question I had is about init-afm position option. it says in the manual: afm init1 = Vector describing the initial position of the spring relative to the reference group. To start a simulation with zero initial force on the pulled group, the initial position should be set to the position of the pulled group relative to the reference group. This sentence is very unclear to me. how do u calculated the poition of the pulled group relative to the referene. Is is by calculating the Center of mass of the pulled group or by calculating the center of mass of the the whole system (pulled group + reference)? Thank you, Belquis Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to obey the stiff spring approximation (which still does NOT mean, you should use a rod ;) ) and therefore shouldn't choose the fc of the spring to small. I usually use a force constant of 500 kJ/mol*nm^2. It actually DOES make sense, to choose a fc comparable to the experiments, you want to compare your sim with, IF you want to compare :) Hope that helps Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rate, AFM_rate), however, for umberalla, there is only two options, a foce constant and position to be specified! my question is: how is the pulling controlled in umberalla sampling option? 2) if I want to do an AFM pulling...what is a reasonalble force constant to use? it seems people are using different K ranging from 10 to 1000's? thank u Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Step size too small
17 aug 2007 kl. 21.46 skrev TJ Piggot: Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules have been successfully minimised on their own so I would suggest that your problem is with either how you edit the .top file or the distance restraint between the molecules. For my protein that has more than one identical chains pdb2gmx does not recognise them as one if you provide different chain identifiers in the pdb file, so doing this should hopefully stop you having to edit the .top file. Yes. Just removing bonds in the top-file is not a good solution. Breaking bonds changes the electronic structure of the molecule, which in turn is represented by different atom types, so you would need to change them as well, depending on the force field. Have you tried the -nomerge option for pdb2gmx? /Erik Hope this helps Tom --On 17 August 2007 19:02 +0200 Per Larsson [EMAIL PROTECTED] wrote: Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_chan ge_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_ precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force =inf on atom 1 Norm of force =inf I would appreciate any advice on how to fix this. Rgds John __ See what you’re getting into?before you go there See it! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 4 out of 8 --- Program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]), VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 1335. It should have been within [ 0 .. 1296 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Thanx for Using GROMACS - Have a Nice Day Error on node 6, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) on CPU 6 out of 8 gcq#10922: Thanx for Using GROMACS - Have a Nice Day * MPI-error in rank 2 Routine MPI_Abort : Terminating after call to MPI_Abort * --- mpimon --- Aborting run after process-2 terminated abnormally Childprocess 17353 exited with exitcode 2 --- gcq#10922: Thanx for Using GROMACS - Have a Nice Day Thankful for some help. Edvin -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? --- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebro, Sweden Tel: +46 19 30 36 69 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? Check out http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation MD simulations are chaotic, and from the same starting point (as measured to single precision) you will observe divergent behaviour, increasingly so as time progresses. The fact that only one of the simulations crash is likely just a numerical artefact. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? Ok (you didn't say that in the first mail...). Does it also happen on one processor? After how many steps does it happen? (see Marks mail). -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error using double precision
Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. that means the trajectory is quite different from SP. I energy minimized the system in d.p. and it is still running after 710 ps. this also changes the trajectory, so the error need not be related to the precision. when it happens again please try to investigate what happened to the structure just before the crash. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. No had stopped at 710 ps... Why is it then working with single precision? -Edvin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. No had stopped at 710 ps... Why is it then working with single precision? You have the possibility of observing different behaviour because the simulation is of a chaotic system. Small changes in starting conditions lead to radical differences later in time. If your starting configuration has some unhappiness that has to relax (as is normal for arbitrarily-solvated biomolecules) under one numerical regime it might explode instantly, under another it might start to relax but some resonant effect leads to problems later, and under yet another it finds the right equilibrium ensemble without breaking. The way to avoid this behaviour is to follow a regime like I recommended in the URL I gave last time. If that is not gentle enough to massage the system into good behaviour (when the topology is correct) then there are further degrees of gentleness you might apply. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topolbuild: attempt at a Gromacs topology builder added to Gromacs user contributed software
I got frustrated with the options for building topologies for ligands and wrote this to allow me to use bond length and angle values derived from prior modeling and NMR data. There probably will be something better than this from the developers at some point, but I decided to upload what I have to Gromacs contributed software. To build a gaff or amber## based topology, the builder requires the antechamber atom type definition files and the gaff and amber## parm files as found in the dat directory for antechamber-1.27 (files in directories dat/antechamber and dat/leap/parm). To build a Tripos force field based topology, the builder requires the TAFF* files found in the Tripos directory pointed to by the Tripos variable $TA_ASCTABLES . The builder has options to renumber atoms and residues to decrease the editing required to add a ligand to a system, to revise atom naming for consistency (only useful with small molecule ligands), and to use bond lengths and angle values derived from coordinates instead of set by the force field. The builder also converts Tripos distance restraints to Gromacs distance restraints. (As noted in the NOT_DONE file in the submission, there seem to be some differences between what Tripos gives as an angle restraint and what Gromacs wants as an angle restraint.) The file is topolbuild.tgz and includes a text file describing the testing I've done so far of topologies built with this program (PROGRAM_TESTING_DONE) along with other descriptive material including indications of possibilities for expansion to other all atom force fields. As noted above, the NOT_DONE file indicates things this contribution does not include. INVENTORY is a list of all files in the contribution. PROGRAM_UNITS lists the program files in the contribution and the purposes they serves, and lists seperately the header files and the program files that call for them. The README should be enough for installation and usage documentation. Note that the antechamber and Tripos force field files are not included in the contribution. These will have to be placed in appropriate directories separately. This contribution does, however, include water and ions force field files suitable for use with gaff. I hope this proves useful to somebody. Sincerely, Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 USA Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. http://autos.yahoo.com/green_center/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error using double precision
[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. No had stopped at 710 ps... Why is it then working with single precision? -Edvin it's difficult to say, it could be coincidence but could also be due to a problem in the software. is this 3.3.1? you are welcome to submit a bugzilla, but we would like to have a system that crashes in ten steps in DP but not in SP... -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] [Fwd: gromacs-gaussian interface compilation - HOW-TO?]
Hi, i want to know the procedure to compile the gromacs-gaussian 03 interface. Can u please give me a link to the installation instructions of gromacs-gaussian 03 interface. I sifted through the gromacs mailing list and google before sending you this question. I am trying to compile on linux i386 machine. I setup all environment variables and then compile gromacs and then gaussian but no interface is developed or no file is present in DEVEL_DIR. I will be thankful for your help. Best regards, Sohail. Pakistan. Have you set the right command line option for configure? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gromacs-gaussian interface compilation - HOW-TO?
Hi, Please post questions like this to the mailing list, so the answers make it to the archive. For QM/MM, have a look at http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/ qmmm.html Unfortunately we are not even allowed to distribute a diff file with modifications to Gaussian (they are _very_ strict on copyright stuff...), but if you ask Gerrit nicely he might have a plain- language description of the modifications necessary. Cheers, Erik On Aug 20, 2007, at 5:14 PM, computer man wrote: Hi, i want to know the procedure to compile the gromacs-gaussian 03 interface. Can u please give me a link to the installation instructions of gromacs-gaussian 03 interface. I sifted through the gromacs mailing list and google before sending you this question. I am trying to compile on linux i386 machine. I setup all environment variables and then compile gromacs and then gaussian but no interface is developed or no file is present in DEVEL_DIR. I will be thankful for your help. Best regards, Sohail. Pakistan. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] nstlist with vdw only
Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/multimessenger gmx_ethane_0365_32768.e74269 Description: Binary data ethane.itp Description: Binary data ethane_32768.top Description: Binary data md.mdp Description: application/mdp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nstlist with vdw only
Hi Nicholas, nstlist=1 means you recalculate the neighborlist every single step, which will be quite expensive. Depending on the type of system and temperature you are simulation you probably want to start somewhere around nstlist=10. Cheers, Erik On Aug 20, 2007, at 10:26 PM, Nicolas Schmidt wrote: Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/ multimessengergmx_ethane_0365_32768.e74269ethane.itpethane_32768. topmd.mdp___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PME or SPME?
Hi all. Well, I have some kind of a didatic doubt: Ok, from what I can understand up to now, PME uses lagrande interpolation for the genaration of the grid, while SPME uses cardinal B-splines to do so. Is it correct? And if, so, gromacs implements PME or SPME (the manual states PME, but also states B-splines)? Thanks a lot in advance! Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] how to get CVS version gmx?
http://wiki.gromacs.org/index.php/CVS_HowTo Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Carsten Kutzner Sent: Saturday, 18 August 2007 12:00 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] how to get CVS version gmx? Hi Linda, you can use these commands to download from CVS: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login Then hit RETURN on password prompt cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx Carsten Zhaoyang Fu wrote: Dear gmx users developers, Would you please let me know how to get the gmx CVS version? I registered in gmx website, however, everytime I try to view the link *instructions on how to access our CVS repository* http://www.gromacs.org/index.php?option=com_contenttask=viewid=80I temid=99, it always says 'You are not authorised to view this resource'. Since gmx3.3.1 has bug in trjconv program, I would like to get the cvs version, which has fixed this problem. Thanks in advance! Linda -- -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Residue abbreviation list with explanations
Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers REMARK 1 pertain to the .dat file from which this file was created, REMARK 1 not to one created from this file: REMARK 1 PDB: 1 2 3 4 REMARK 1 MMOD: 1 2 3 4 / HETATM1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0 HETATM2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0 HETATM3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0 HETATM4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0 CONECT134 CONECT12 CONECT12 CONECT21 CONECT21 CONECT31 CONECT41 END Thank you in advance - Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME or SPME?
Jones de Andrade wrote: Hi all. Well, I have some kind of a didatic doubt: Ok, from what I can understand up to now, PME uses lagrande interpolation for the genaration of the grid, while SPME uses cardinal B-splines to do so. Is it correct? And if, so, gromacs implements PME or SPME (the manual states PME, but also states B-splines)? SPME. The GROMACS manual refers to the algorithm in ref 10 of the manual as PME, even though it is a modification of the original algorithm in ref 9, and that modification is often referred to as smooth PME. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Residue abbreviation list with explanations
Sagittarius wrote: Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers REMARK 1 pertain to the .dat file from which this file was created, REMARK 1 not to one created from this file: REMARK 1 PDB: 1 2 3 4 REMARK 1 MMOD: 1 2 3 4 / HETATM1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0 HETATM2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0 HETATM3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0 HETATM4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0 CONECT134 CONECT12 CONECT12 CONECT21 CONECT21 CONECT31 CONECT41 END Um no, you don't need a residue abbreviation list. See http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Residue abbreviation list with explanations
Could you please help me to find a Residue abbreviation list web site. If you want to find out what people are calling a particular molecule or residue, best place to look is the PDB Database. If it is a small molecule, then http://alpha2.bmc.uu.se/hicup/ is a good place to look. However, as indicated previously, this is not what your current issue is. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
