Re: [gmx-users] setup problem
thank you for your suggestions. actually i tried all -pbc options, but neither did help. but i think i found the solution in an old posting from ka feenstra. there he writes that due to efficiency (iirc) at least one atom of each part of the system has to be in the rectangular waterbox. therefore the translation i think. so rotating my protein such that the ligand is at least partly immersed in the solvent helped to solve the problem. actually i could have found the solution in the manual, chapter 3, as well. seems to be worth reading that in-depth ;) Original-Nachricht Datum: Wed, 07 Mar 2007 11:20:22 +1100 Von: Mark Abraham [EMAIL PROTECTED] An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Betreff: Re: [gmx-users] setup problem merc mertens wrote: hello, i have got a problem with my simulation setup. i prepare a protein with two ligands in a dodecahedral box. after the setup the ligands are situated in the active site of the protein all right. when i look at the structure after em one of the ligands is now outside the protein in the solvent. if i generate symmetry mates the ligand is perfectly at its typical position in the active site of the next symmetry related molecule. yet the flag -pbc nojump in trjconv does not produce a whole molecule!! therefore it seems that the ligand is translated during the em step. when i look at the structure before em i see that the ligand is outside the solventbox (but inside the dodecahedral box!!!) and translated inside the solventbox after em. unfortunately i have no idea how to solve this problem except to make the box so huge, that calculation becomes too time consuming, as the protein is a tetramer with nearly 1500 residues. Have you tried the trjconv option that puts the COM of each molecule (or residue, I forget) inside the box? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen downloaden: http://www.gmx.net/de/go/browser ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] positive system total-energy
Hi David, Thanks for your reply! It is a pure ionic liquid system. I compared this energy result with that of another system, found that the term of Coul.-recip. is very smaller (- 4664.24) than another system's result (-56014.1). All other terms of the energy are in the same order of magnitute. What does Coul.-recip mean? PME is used for Coulomb interaction. Switch is used for LJ interaction. 1. abnormal result Energy Average RMSD Fluct. Drift Tot-Drift --- Bond8121.16129.568129.564 0.000320592 3.20592 Angle 16284.9174.598174.578 -0.00090818- 9.0818 Ryckaert-Bell. 4489.18147.842144.019 -0.0115717 -115.717 LJ-141169.9734.081833.9909 -0.000861911 - 8.61912 Coulomb-14 2666.03191.396186.964 -0.0141849 -141.849 LJ-(SR)-32381.8146.511 146.4 -0.0019765- 19.765 Disper.-corr. -2462.415.292795.28651 8.934e-05 0.8934 Coulomb-(SR) -11046.1213.609210.484 0.0126112126.112 Coul.-recip. -4664.24 141.26136.108 0.0130948 130.948 Potential -17823.3250.663250.472 -0.00338716 - 33.8716 Kinetic-En.32678.4188.545188.545 -6.01562e-06 - 0.0601562 Total-Energy 14855.1163.416163.122 -0.00339318 - 33.9318 Temperature299.9651.730711.73071 0 0 2.normal results Energy Average RMSD Fluct. Drift Tot-Drift --- Bond3707.66103.252103.238 0.000572337 5.7156 Angle 10644.9157.095157.095 4.14791e-06 0.0414228 Ryckaert-Bell. 3215.44108.937108.932 -0.000366312 - 3.65815 LJ-14 1314.1929.530329.5302 -3.01152e-05 - 0.300743 Coulomb-14 -14049.817.410417.4061 0.0001343981.34216 LJ-(SR)-11648.8158.786 158.35 0.00408289 40.7735 Disper.-corr. -1192.913.766083.73988 0.000153815 1.53606 Coulomb-(SR) -31913.4149.436148.956 0.004152841.4716 Coul.-recip. -56014.136.376436.0691 0.00163665 16.3442 Potential -95936.8248.465 246.67 0.0103406 103.266 Kinetic-En.23457.6186.095186.095 1.29671e-05 0.129495 Total-Energy -72479.2162.228159.458 0.0103536 103.395 Temperature 399.9283.172723.17272 2.21097e-07 0.00220797 2007/3/6, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Hi, I have a 10 ns job. But when using the g_energy to calculate the component of the energy, I got a positive total-energy!! Who can give some suggestions? Thanks a lot! what kind of system? do you happen to have an organic solvent? in that case you should subtract the self energy per molecule -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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 -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Which force-field for DNA-protein complex ?
I'm currently using AMBER03 for a DNA-protein complex. A little bit of struggle and extra examination of topologies and such was needed when setting up the system, but nothing too daunting. /Erik 7 mar 2007 kl. 01.12 skrev mathieu coincon: I searched the database in order to choose which ff I should use. But I would like to have feadback from people used to such simulations. Thanks by advance --- Mathieu Coincon PhD Student Universite de Montreal (+1)514-343-6111 #5352 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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: Atom index (1) in settles out of bounds (1-0)
Sorry, I digged through the post-list of old user-questions and found the same problem occuring. the answer to the question was written by David v.d.Spoel and was: the position in the top file where the spc.itp was included is wrong. In my top file this include statement is at the end of the script. Where should it be ? Thanks Joern -- Forwarded Message -- Subject: Atom index (1) in settles out of bounds (1-0) Date: Wednesday 07 March 2007 10:53 From: Joern Lenz [EMAIL PROTECTED] To: gmx-users@gromacs.org Dear users, I have a question regarding a simulation (using the amber ports) of DNA covalently bound to a protein. First of all I made an entry in the specbond.dat and the bond was correctly build between the a P of the DNA and a Tyr of the protein. After that I started grompp and got the following error: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file .../bin/x86_64-unknown-linux-gnu/share/gromacs/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) the content of the spc.itp file in line 41 is (marked with ==: #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OWfunct doh dhh == 1 1 0.1 0.16330 Can anyone tell me how to avoid this error and go on with simulations ? Many thanks in advance Joern --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Atom index (1) in settles out of bounds (1-0)
Dear users, I have a question regarding a simulation (using the amber ports) of DNA covalently bound to a protein. First of all I made an entry in the specbond.dat and the bond was correctly build between the a P of the DNA and a Tyr of the protein. After that I started grompp and got the following error: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file .../bin/x86_64-unknown-linux-gnu/share/gromacs/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) the content of the spc.itp file in line 41 is (marked with ==: #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OWfunct doh dhh == 1 1 0.1 0.16330 Can anyone tell me how to avoid this error and go on with simulations ? Many thanks in advance Joern ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gmxcheck and trjconv
Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gmxcheck and trjconv
andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea is the simulation still running? then file buffering may play in. alt. if you kill -9 then the buffers will not be flushed. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] positive system total-energy
Qiao Baofu wrote: Hi David, Thanks for your reply! It is a pure ionic liquid system. I compared this energy result with that of another system, found that the term of Coul.-recip. is very smaller (-4664.24) than another system's result (- 56014.1). All other terms of the energy are in the same order of magnitute. What does Coul.-recip mean? Energy from PME. Please do a simulation of a single ion in vacuum (same box size) and from that determine the single molecule energy. You have to subtract this N times from your potential energy. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] gmxcheck and trjconv
Hi nope they are both finished. I have also checked the edr files and the time does not correspond to the time found in the respectively trr files. Those MD are carried out in a supercomputer (SARA in Amsterdam) and they were killed by the queue system. Probably as you said a buffer problem ... gmx version 3.3.1 Regards andrea David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea is the simulation still running? then file buffering may play in. alt. if you kill -9 then the buffers will not be flushed. -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gmxcheck and trjconv
Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea is the simulation still running? then file buffering may play in. alt. if you kill -9 then the buffers will not be flushed. -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gmxcheck and trjconv
andrea spitaleri wrote: Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea is the simulation still running? then file buffering may play in. alt. if you kill -9 then the buffers will not be flushed. buffering is separate per file. in trr you have only half a frame. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] g_rdf
Hi, I'm using g_rdf to calculate the RDF of a system. The r range ends at 3nm. I would like to change it to 100nm but it seems that there are no option for it. Can you help me ? thanks, marco -- Marco Cammarata, Post-Doc European Synchrotron Radiation Facility Material Science Group 6, rue Jules Horowitz BP 220, Grenoble Cedex 38043, FRANCE Beamline ID09b Office : +33 (0)4 76 88 29 37 Beamline : +33 (0)4 76 88 26 95 Fax : +33 (0)4 76 88 27 43 email: [EMAIL PROTECTED] http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID09B/ http://www.fisica.unipa.it/~emoglobina/marco ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] limitations in the umbrella sampling
From: Seungho Choe [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] limitations in the umbrella sampling Date: Tue, 06 Mar 2007 17:33:38 -0500 Dear all, In the manual, it says : If a group contains part of a molecule of which the bondlengths are constrained, the results may be unreliable. I'm a little confused. Let's think of the following two cases (A: the reference group, B: a group which will be pulled) : 1) A(partially constrained) + B (no constraints) 2) A(no constraints) + B(partially constrained) Does it mean that both pmf calculations are not reliable ? Should I use the free energy code for both cases ? Any comments would be appreciated. Thank you. If you read the manual more carefully you can see that this restriction only applies to constraint pulling, not umbrella pulling. Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_rdf
marco cammarata wrote: Hi, I'm using g_rdf to calculate the RDF of a system. The r range ends at 3nm. I would like to change it to 100nm but it seems that there are no option for it. Can you help me ? thanks, marco The CVS version has an option to turn off the periodic boundary conditions. That only makes sense in special cases though. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] g_rdf
2007/3/7, marco cammarata [EMAIL PROTECTED]: Hi, I'm using g_rdf to calculate the RDF of a system. The r range ends at 3nm. r range ends at 3nm because (your box size)/2 is 3 nm I would like to change it to 100nm but it seems that there are no option for it. 100 nm? Are you sure? it is much biggger than your box size, so you will have some pairs between an atom and itself (in other boxs). If you really want so, you can change some lines in the gmx_rdf.c. Can you help me ? thanks, marco -- Marco Cammarata, Post-Doc European Synchrotron Radiation Facility Material Science Group 6, rue Jules Horowitz BP 220, Grenoble Cedex 38043, FRANCE Beamline ID09b Office : +33 (0)4 76 88 29 37 Beamline : +33 (0)4 76 88 26 95 Fax : +33 (0)4 76 88 27 43 email: [EMAIL PROTECTED] http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID09B/ http://www.fisica.unipa.it/~emoglobina/marco ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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: Re: [gmx-users] vacuum right but melt collapse
Hi Ji Qing, Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, by hand, checking all bonds, angles, dihedrals, exclusion (implicit ones!), etc. Good luck, Tsjerk On 3/7/07, kitty ji [EMAIL PROTECTED] wrote: Thanks Mark. But when one polymer chain was used, non-bonded interaction has already been there. Because one chain means C44H156O22. After all, I'd like to try more chains. Message: 1 Date: Tue, 06 Mar 2007 17:01:52 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] vacuum right but melt collapse To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=GB2312 kitty ji wrote: Hi GMX user: A model for Poly(vinyl methyl ether) was built with OPLS force field ( all H ). When the model was run alone (a single chain) in vacuum, anything goes ok. But with 45 chains box, the system will be collapse with a little bond elongates abnormal whatever in NVT or NPT. The relax time of pressure and temperature were adjust but no helpful. How can I found some possible reason and then fix it ? Any advise will be appreciated. If an isolated molecule doesn't do anything strange, and two more more do, then you have a problem with inter-molecular interactions, i.e. the non-bonded ones. Try with just 2 chains to verify this... and look carefully at the atom types and the non-bonded parameters for them. Mark * Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ，82618423 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] setup problem
Hi Merc, Probably, the .tpr file you used for trjconv -pbc nojump already had the ligand jumped. In that case, you will find all frames consistently having a shift between the ligand and the protein. Make sure you use a reference which has the ligand in place (the .pdb or .gro file you used to set up the system for example). Oh, and do read about periodic boundary conditions. Best, Tsjerk On 3/7/07, merc mertens [EMAIL PROTECTED] wrote: thank you for your suggestions. actually i tried all -pbc options, but neither did help. but i think i found the solution in an old posting from ka feenstra. there he writes that due to efficiency (iirc) at least one atom of each part of the system has to be in the rectangular waterbox. therefore the translation i think. so rotating my protein such that the ligand is at least partly immersed in the solvent helped to solve the problem. actually i could have found the solution in the manual, chapter 3, as well. seems to be worth reading that in-depth ;) Original-Nachricht Datum: Wed, 07 Mar 2007 11:20:22 +1100 Von: Mark Abraham [EMAIL PROTECTED] An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Betreff: Re: [gmx-users] setup problem merc mertens wrote: hello, i have got a problem with my simulation setup. i prepare a protein with two ligands in a dodecahedral box. after the setup the ligands are situated in the active site of the protein all right. when i look at the structure after em one of the ligands is now outside the protein in the solvent. if i generate symmetry mates the ligand is perfectly at its typical position in the active site of the next symmetry related molecule. yet the flag -pbc nojump in trjconv does not produce a whole molecule!! therefore it seems that the ligand is translated during the em step. when i look at the structure before em i see that the ligand is outside the solventbox (but inside the dodecahedral box!!!) and translated inside the solventbox after em. unfortunately i have no idea how to solve this problem except to make the box so huge, that calculation becomes too time consuming, as the protein is a tetramer with nearly 1500 residues. Have you tried the trjconv option that puts the COM of each molecule (or residue, I forget) inside the box? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen downloaden: http://www.gmx.net/de/go/browser ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gmxcheck and trjconv
Hey Andrea, Also note that you have 70 FRAMES with 1 ps time step. That means, with the first frame at t=0, that you have a maximum time of (70-1)*1 ps = 69 ps in the output. Ciao! Tsjerk On 3/7/07, David van der Spoel [EMAIL PROTECTED] wrote: andrea spitaleri wrote: Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea is the simulation still running? then file buffering may play in. alt. if you kill -9 then the buffers will not be flushed. buffering is separate per file. in trr you have only half a frame. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] limitations in the umbrella sampling
Thanks a lot. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gmxcheck and trjconv
Hi Tsjerk, true i have to remember to start to count from 0 ... as usual :P thanks andrea Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) - Original Message - From: Tsjerk Wassenaar [EMAIL PROTECTED] Date: Wednesday, March 7, 2007 5:56 pm Subject: Re: [gmx-users] gmxcheck and trjconv Hey Andrea, Also note that you have 70 FRAMES with 1 ps time step. That means, with the first frame at t=0, that you have a maximum time of (70-1)*1 ps = 69 ps in the output. Ciao! Tsjerk On 3/7/07, David van der Spoel [EMAIL PROTECTED] wrote: andrea spitaleri wrote: Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards andrea is the simulation still running? then file buffering may play in. alt. if you kill -9 then the buffers will not be flushed. buffering is separate per file. in trr you have only half a frame. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 begin:vcard n:Spitaleri;Andrea fn:Andrea Spitaleri tel;fax:+390226434153 org:Dibit Scientific Insititute;BioMolecular Structure adr:;;via Olgettina 58;Milan;;24132;Italy version:2.1 email;internet:[EMAIL PROTECTED] title:Dr end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] genbox give coord file more waters than top file
Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read man genbox, choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, epsilon_rf and dielectric constant calculation
Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? 2. Whet is the best way to calculate the dielectric constant of the simulation box, does g_dipole is enough or should I use g_dielectric also. Best, Itamar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, epsilon_rf and dielectric constant calculation
Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? Have you looked in section 7.3? 2. Whet is the best way to calculate the dielectric constant of the simulation box, does g_dipole is enough or should I use g_dielectric also. I don't know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, epsilon_rf and dielectric constant calculation
Dear Mark, I read the manual few times looking for a clue. The only thing I could understand it that epsilon_rf is not taking inti account if I don't use reaction field. Best, Itamar. Mark Abraham wrote: Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? Have you looked in section 7.3? 2. Whet is the best way to calculate the dielectric constant of the simulation box, does g_dipole is enough or should I use g_dielectric also. I don't know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Prediction is very difficult, especially about the future - Niels Bohr === | Itamar Kass | Postdoctoral Research Fellow | | Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3346 9922 | Fax: +61 7 3365 3872 | email: [EMAIL PROTECTED] Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, epsilon_rf and dielectric constant calculation
Dear Mark, I read the manual few times looking for a clue. The only thing I could understand it that epsilon_rf is not taking inti account if I don't use reaction field. 7.3.9 clearly says epsilon_rf: (1) The relative dielectric constant of the reaction field. This is only used with reaction-field electrostatics. A value of 0 means infinity. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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: Re: [gmx-users] vacuum right but melt collapse
Tsjerk Wassenaar, thank you very much for you suggestion even if most of them have been manipulated. Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, by hand, checking all bonds, angles, dihedrals, exclusion (implicit ones!), etc. when the explosion happened, the energy of bond, angle and potential will were increase. And the topology has been checked several times. Now I increase the cutoff of VDW Coulomb from 0.9 to 1.5. The system looks ok from last night to this time. If the problem is fixed, I conclude that cutoff 0.9 is not enough for electric system. Hope this conclusion is helpful for GMX users. Message: 2 Date: Wed, 7 Mar 2007 17:49:30 +0100 From: Tsjerk Wassenaar [EMAIL PROTECTED] Subject: Re: Re: [gmx-users] vacuum right but melt collapse To: kitty ji [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=GB2312; format=flowed Hi Ji Qing, Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, by hand, checking all bonds, angles, dihedrals, exclusion (implicit ones!), etc. Good luck, Tsjerk On 3/7/07, kitty ji [EMAIL PROTECTED] wrote: Thanks Mark. But when one polymer chain was used, non-bonded interaction has already been there. Because one chain means C44H156O22. After all, I'd like to try more chains. Message: 1 Date: Tue, 06 Mar 2007 17:01:52 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] vacuum right but melt collapse To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=GB2312 kitty ji wrote: Hi GMX user: A model for Poly(vinyl methyl ether) was built with OPLS force field ( all H ). When the model was run alone (a single chain) in vacuum, anything goes ok. But with 45 chains box, the system will be collapse with a little bond elongates abnormal whatever in NVT or NPT. The relax time of pressure and temperature were adjust but no helpful. How can I found some possible reason and then fix it ? Any advise will be appreciated. If an isolated molecule doesn't do anything strange, and two more more do, then you have a problem with inter-molecular interactions, i.e. the non-bonded ones. Try with just 2 chains to verify this... and look carefully at the atom types and the non-bonded parameters for them. Mark * Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 £¬82618423 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
