[gmx-users] Problem wih Fe-S cluster
Hi everyone I am facing a problem with derivation of parameters of Fe-S cluster in a protein.Can anybody please tell me for deriving a parameters do I have to consider the co-ordinates of a typical fe-s cluster as there in Protein Data Base (PDB) or the co-ordinates of the Fe-S cluster present in my protein of interest. Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.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/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/mailing_lists/users.php
[gmx-users] Can N(CH2)3 be set a charge group?
Dear gmx users, Can N(CH2)3 be set a charge group? Is it too large to set? Any reply would be thanked very much. Sincerely Chaofu Wu _ 打工，挣钱，买房子，快来MClub一起”金屋藏娇”！ http://club.msn.cn/?from=10___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Can N(CH2)3 be set a charge group?
Hi, I don't think that is a good idea. I put the following advise in grompp Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n For efficiency and accuracy, charge group should consist of a few atoms.\n For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.,' We should also put this somewhere in the manual. Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Date: Thu, 25 Jun 2009 15:28:08 +0800 Subject: [gmx-users] Can N(CH2)3 be set a charge group? Dear gmx users, Can N(CH2)3 be set a charge group? Is it too large to set? Any reply would be thanked very much. Sincerely Chaofu Wu 把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！ _ See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem wih Fe-S cluster
Hi Subarna, If you just want to retain the structure of the cluster it doesn't matter too much. It may be good to average values from different structures, though. HOWEVER, an FeS cluster is a catalytic site, which probably has fancy electronic properties, which may well affect the behaviour of the surrounding protein. If you are interested in the protein dynamics, you want to describe it properly. Doing so requires proper parameterization, ergo performing quantum mechanical calculations with validation against experimental data, ergo doing a lot of work. This is not something for a lazy Sunday afternoon! Cheers, Tsjerk On Thu, Jun 25, 2009 at 7:55 AM, subarna thakurthakur.suba...@yahoo.co.in wrote: Hi everyone I am facing a problem with derivation of parameters of Fe-S cluster in a protein.Can anybody please tell me for deriving a parameters do I have to consider the co-ordinates of a typical fe-s cluster as there in Protein Data Base (PDB) or the co-ordinates of the Fe-S cluster present in my protein of interest. Subarna ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: problems with some calculated trajectories
1) trjconv with the -pbc nojump option does not help - it removes most of the jumps but one big remains- the rmsd for the trajectory is http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg before the converting with -pbc and http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg after conversion. interestingly under linux vmd could load the trajectories which look like that: http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg and http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg 2) Here an illustration for other trajectories with the same problem: http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg 3) gmxcheck returns no error, just this: trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 167731 Reading frame 2 time 6.000 Item#frames Timestep (ps) Step 202613 Time 202613 Lambda 202613 Coords 202613 Velocities202730 Forces202730 Box 202613 any further ideas what I could do with those trajectories or what I shall do to avoid such problems in future (integration step, water shell size, ... ?) cheers Bernhard -- Message: 4 Date: Mon, 22 Jun 2009 16:37:44 +0200 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] problems with some calculated trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a3f9738.7070...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ? /Erik -- Message: 2 Date: Mon, 22 Jun 2009 17:19:43 +0200 From: Martin H?fling martin.hoefl...@lmu.de Subject: Re: [gmx-users] problems with some calculated trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 806bd6cf-4903-465f-a2b6-8d0ffa984...@lmu.de Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. Reasons for damaged trajectories, even when gromacs runs through fine... ... for me - filesystem issues were causing this. In particular this happened for me with NFS shares and on Lustre filesystems. My NFS problems got solved with an upgrade of the NFS packages on our machines (at least 1 1/2 yrs ago). Best Martin -- Message: 3 Date: Mon, 22 Jun 2009 18:06:13 +0200 From: Martin H?fling martin.hoefl...@gmx.de Subject: Re: [gmx-users] problems with some calculated trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: d1212df6-6341-45d3-8ef6-f975b68ce...@gmx.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Am 22.06.2009 um 17:19 schrieb Martin Höfling: Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. ^ ^^ = gmxcheck :-) Best Martin -- Message: 4 Date: Mon, 22 Jun 2009 13:29:10 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users]-bash: /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash:No such file or directory To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a3fbf66.4010...@vt.edu Content-Type: text/plain; charset=GB2312 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: problems with some calculated trajectories
Hi Bernhard, The images, are they taken from exactly the same angle? If so, there's some change in orientation that is just impossible in such a short time. You didn't happen to fit your structure to a reference prior to removal of jumps, did you? Fitting messes up PBC and garbles results from -pbc nojump. If these are not from the original trajectory (mdrun output), have a look what happens there. Otherwise, trace back all your steps. Maybe paste here what you've done exactly... Cheers, Tsjerk On Thu, Jun 25, 2009 at 10:10 AM, Bernhard Knappbernhard.kn...@meduniwien.ac.at wrote: 1) trjconv with the -pbc nojump option does not help - it removes most of the jumps but one big remains- the rmsd for the trajectory is http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg before the converting with -pbc and http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg after conversion. interestingly under linux vmd could load the trajectories which look like that: http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg and http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg 2) Here an illustration for other trajectories with the same problem: http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg 3) gmxcheck returns no error, just this: trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 # Atoms 167731 Reading frame 2 time 6.000 Item #frames Timestep (ps) Step 20261 3 Time 20261 3 Lambda 20261 3 Coords 20261 3 Velocities 2027 30 Forces 2027 30 Box 20261 3 any further ideas what I could do with those trajectories or what I shall do to avoid such problems in future (integration step, water shell size, ... ?) cheers Bernhard -- Message: 4 Date: Mon, 22 Jun 2009 16:37:44 +0200 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] problems with some calculated trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a3f9738.7070...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ? /Erik -- Message: 2 Date: Mon, 22 Jun 2009 17:19:43 +0200 From: Martin H?fling martin.hoefl...@lmu.de Subject: Re: [gmx-users] problems with some calculated trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 806bd6cf-4903-465f-a2b6-8d0ffa984...@lmu.de Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. Reasons for damaged trajectories, even when gromacs runs through fine... ... for me - filesystem issues were causing this. In particular this happened for me with NFS shares and on Lustre filesystems. My NFS problems got solved with an upgrade of the NFS packages on our machines (at least 1 1/2 yrs ago). Best Martin -- Message: 3 Date: Mon, 22 Jun 2009 18:06:13 +0200 From: Martin H?fling martin.hoefl...@gmx.de Subject: Re: [gmx-users] problems with some calculated trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: d1212df6-6341-45d3-8ef6-f975b68ce...@gmx.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Am 22.06.2009 um 17:19 schrieb Martin Höfling: Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. ^ ^^ = gmxcheck :-) Best Martin -- Message: 4 Date: Mon, 22 Jun 2009 13:29:10 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] -bash: /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash:No such file or directory To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a3fbf66.4010...@vt.edu Content-Type: text/plain; charset=GB2312 ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. 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
Re: [gmx-users] Re: Re: problems with some calculated trajectories
Bernhard Knapp wrote: 1) trjconv with the -pbc nojump option does not help - it removes most If I understand correctly, -pbc nojump will help when the relevant atoms are part of the same [moleculetype]. One fragment in each of your two examples is apparently the same four-strand sheet with helix wrapped around it. This suggests to me that you might have several chains, each as a different [moleculetype] and your observations are actually what you should expect. If so, -pbc cluster is the kind of thing you should be using. In any case, a description of the composition of your system and copies of a series of commands that reproduces your result would always have been appropriate :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Re: Re: problems with some calculated trajectories
Date: Thu, 25 Jun 2009 18:39:53 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Re: Re: problems with some calculated trajectories Bernhard Knapp wrote: 1) trjconv with the -pbc nojump option does not help - it removes most If I understand correctly, -pbc nojump will help when the relevant atoms are part of the same [moleculetype]. One fragment in each of your two examples is apparently the same four-strand sheet with helix wrapped around it. This suggests to me that you might have several chains, each as a different [moleculetype] and your observations are actually what you should expect. If so, -pbc cluster is the kind of thing you should be using. You did not understand correctly :) -pbc nojump removes periodic jumps of atoms, it does not now about molecules. The effect is that no periodic jumps occur from the reference structure (either tpr or first frame). This means, for instance, that protein complexes will stay intact and that water will diffuse out of the box in visualization. Berk In any case, a description of the composition of your system and copies of a series of commands that reproduces your result would always have been appropriate :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem in energy minimization for a empty membrane system
Hi! Thanks a alot for all the suggestions i've got from Justin and Mark. I found out that i actually deleted the box information from the starting structure PDB. Once i put it back, It worked. However, it stopped with this message. Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.trr to ./#em.trr.19# Back Off! I just backed up em.gro to ./#em.gro.11# Steepest Descents converged to machine precision in 76 steps, but did not reach the requested Fmax 1000. Potential Energy = -2.24796600790506e+05 Maximum force = 1.14539522791599e+03 on atom 6619 Norm of force = 1.62353061702859e+04 Is it mean that the minimization is done and is already converged? Here the result for the final Step 75. Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. Improper Dih. 1.23491e+039.85552e+034.48086e+034.81663e+031.33894e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 4.09985e+038.28955e+03 -1.68827e+04 -1.04035e+05 -1.38691e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 6.95754e+02 -2.24797e+050.0e+00 -2.24797e+050.0e+00 Pressure (bar) 0.0e+00 The position restraint is working fine as well Thank you so much. Regards, ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in energy minimization for a empty membrane system
Bing Bing wrote: Hi! Thanks a alot for all the suggestions i've got from Justin and Mark. I found out that i actually deleted the box information from the starting structure PDB. Once i put it back, It worked. However, it stopped with this message. Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) That can be normal. writing lowest energy coordinates. Back Off! I just backed up em.trr to ./#em.trr.19# Back Off! I just backed up em.gro to ./#em.gro.11# Steepest Descents converged to machine precision in 76 steps, but did not reach the requested Fmax 1000. Potential Energy = -2.24796600790506e+05 Maximum force = 1.14539522791599e+03 on atom 6619 Norm of force = 1.62353061702859e+04 Is it mean that the minimization is done and is already converged? Here the result for the final Step 75. Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. Improper Dih. 1.23491e+039.85552e+034.48086e+034.81663e+031.33894e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 4.09985e+038.28955e+03 -1.68827e+04 -1.04035e+05 -1.38691e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 6.95754e+02 -2.24797e+050.0e+00 -2.24797e+050.0e+00 Pressure (bar) 0.0e+00 These all seem plausible. The proof is in MD running in a stable fashion. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Re: Re: Re: problems with some calculated trajectories
The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope, T-cell receptor alpa, T-cell receptor beta). What you can see in http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg is exactly the same angle. The two MHC chains jump away from each other and from the T-cell receptor. I have already simulated some of these complexes before with slightly different amino acid sequences but with an overall similar structure and this jumping never occured. I did the following conversion: trjconv -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -o 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -n index.ndx -pbc nojump -novel -fit progressive -skip 10 and the rmds calculation with g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o rmsd.TcrCdrs.noJump.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 7 but also if I calculate the rmsd directly from the trr-file the jumps are inside and the same as from the xtc file without -pbc nojump g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o rmsd.TcrCdrs.fitpMHC.FromOriginalTRR.xvg -n index.cdrsAndStrands.ndx -ng 7 cheers Bernhard Today's Topics: 1. Re: Re: Re: problems with some calculated trajectories (Tsjerk Wassenaar) 2. Re: Re: Re: problems with some calculated trajectories (Mark Abraham) 3. RE: Re: Re: problems with some calculated trajectories (Berk Hess) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pullx.xvg Meaning of output?
What is meant by absolute reference? Can it be the Origin (0, 0, 0). Does it assume a random reference point for the pullx.xvg? I get a negative value for my first pulling group, even though it is inside the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't fit either. Does it make any difference if I use reference_group = system or no reference group at all? Or what else do you usually use as a reference group? What does the reference group do during the simulation? I understand that pulling from both sides, Gromacs puts a spring at each pullgroup. Is there any restraint on the reference group? Cheers, Ilona Quoting Berk Hess g...@hotmail.com: Hi, In most cases you shoud NOT use an absolute reference. In plain MD there is not absolute reference, therefore pulling without a reference group is a recipe for trouble. By default center of mass motion removal will be turned on, in which case you are pulling against the center of mass of the whole system. If you have solvent, thermodynamically the pulling will have no effect, since the protein can move along, if you pull slow enough. If you pull too fast (which is very likely), you will get horrendous artifacts. Berk Date: Thu, 25 Jun 2009 11:02:41 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: g...@hotmail.com Subject: RE: [gmx-users] pullx.xvg Meaning of output? Hi Berk, I am trying to unfold a protein by stretching/pulling it from both sides in Z (and -Z) direction. To this end, I am trying to figure out the best parameters. If I understand you correctly, it should not make any difference to the pulling itself, i.e. the forces the protein experiences, whether a reference group is chosen or not. Unfortunately, my simulations show something different: I did exactly the same pulling simulation twice, using a backbone atom as reference group in the first case and no reference group in the second case. The differences I found are as follows: When I use no reference group, the molecule center moves less along the Z axis than in case of a defined reference group. The reason I do bother about that fact is that I do not want my molecule to leave the box on one end due to pulling effects even though the box is more than 3 nm longer than the unfolded protein. Also, pullf.xvg shows quite similar values for the simulation without reference group whereas forces differ more if a reference group is used. (see attached files). Why is that so? Best wishes, Ilona Quoting Berk Hess g...@hotmail.com: Hi, Everything depends on what you want to accomplish, which you do not write. I don't see why you would want to look at single atoms. Since you pull on COM's, only the COM coordinates are relevant. If you want to look at single atoms, simply store them in the xtc file. If you have only two groups, there is no physical difference between the reference group and the first pull group. They are simply two groups between which the distance is calculated and the forces act. If you used an absolute reference, 0Z is the absolute reference coordinate, not the coordinate of a group. Berk Date: Tue, 23 Jun 2009 14:39:48 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: gmx-users@gromacs.org Subject: RE: [gmx-users] pullx.xvg Meaning of output? Dear Berk, Thanks for the quick reply. That leads me to my next questions: *I used the whole N and C residues for pulling. Is there any way of reconstructing the values for the single atoms? Or do you recommend only to pull N and C in the first place? *What does the reference group actually do? Can I simply leave it out? Does it influence pulling? What would be a good reference group? A random backbone atom from the middle of the protein? I'm looking forward to your reply. Thank you very much in advance. Best wishes, Ilona Quoting Berk Hess g...@hotmail.com: Hi, This is actually not (yet) documented. 0Z is the Z-coordinate of group 0. 1dZ is the the Z-coordinate of group 1 minus the one of group 0. Berk Date: Tue, 23 Jun 2009 12:54:37 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: gmx-users@gromacs.org Subject: [gmx-users] pullx.xvg Meaning of output? Hi! I am trying to understand the output of my pulling simulation: I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ. Since the website is down I cannot check on previous issues, so sorry for asking the same question again as I already asked last week but which remained unanswered. I would appreciate any advice. Thanks a lot. Ilona ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Re: Re: Re: Re: problems with some calculated trajectories
Bernhard Knapp skrev: The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope, T-cell receptor alpa, T-cell receptor beta). What you can see in http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg is exactly the same angle. The two MHC chains jump away from each other and from the T-cell receptor. I have already simulated some of these complexes before with slightly different amino acid sequences but with an overall similar structure and this jumping never occured. I did the following conversion: trjconv -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -o 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -n index.ndx -pbc nojump -novel -fit progressive -skip 10 As Tsjerk stated earlier, fitting prior to jump-removal can mess up the trajectory. Try without -fit. g_rms will superimpose the structures for you anyway. and the rmds calculation with g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o rmsd.TcrCdrs.noJump.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 7 but also if I calculate the rmsd directly from the trr-file the jumps are inside and the same as from the xtc file without -pbc nojump g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o rmsd.TcrCdrs.fitpMHC.FromOriginalTRR.xvg -n index.cdrsAndStrands.ndx -ng 7 cheers Bernhard Today's Topics: 1. Re: Re: Re: problems with some calculated trajectories (Tsjerk Wassenaar) 2. Re: Re: Re: problems with some calculated trajectories (Mark Abraham) 3. RE: Re: Re: problems with some calculated trajectories (Berk Hess) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. 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 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] use of LAN for parallel processing
Thanks gromacs for you replay, can any body provide tutorial/standard protocol how to use of LAN for parallel processing. AKALABYA BISSOYI N.I.T.Rourkela ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pullx.xvg Meaning of output?
Hi, As I said, if you set a reference group (any name/group for pull_group0), you apply a potential between two groups group0 and group1. These two groups are treated completely equivalently (they both experience the same force, but with opposite sign and they will both move under influence of the force). If you use an absolute reference (no name for pull_group0), the reference is (0,0,0) plus pull_init. There is only pull group, so only one group will move. But remember that the rest of the system will move in the other direction if you remove COM motion. Berk Date: Thu, 25 Jun 2009 14:08:48 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: gmx-users@gromacs.org Subject: RE: [gmx-users] pullx.xvg Meaning of output? What is meant by absolute reference? Can it be the Origin (0, 0, 0). Does it assume a random reference point for the pullx.xvg? I get a negative value for my first pulling group, even though it is inside the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't fit either. Does it make any difference if I use reference_group = system or no reference group at all? Or what else do you usually use as a reference group? What does the reference group do during the simulation? I understand that pulling from both sides, Gromacs puts a spring at each pullgroup. Is there any restraint on the reference group? Cheers, Ilona Quoting Berk Hess g...@hotmail.com: Hi, In most cases you shoud NOT use an absolute reference. In plain MD there is not absolute reference, therefore pulling without a reference group is a recipe for trouble. By default center of mass motion removal will be turned on, in which case you are pulling against the center of mass of the whole system. If you have solvent, thermodynamically the pulling will have no effect, since the protein can move along, if you pull slow enough. If you pull too fast (which is very likely), you will get horrendous artifacts. Berk Date: Thu, 25 Jun 2009 11:02:41 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: g...@hotmail.com Subject: RE: [gmx-users] pullx.xvg Meaning of output? Hi Berk, I am trying to unfold a protein by stretching/pulling it from both sides in Z (and -Z) direction. To this end, I am trying to figure out the best parameters. If I understand you correctly, it should not make any difference to the pulling itself, i.e. the forces the protein experiences, whether a reference group is chosen or not. Unfortunately, my simulations show something different: I did exactly the same pulling simulation twice, using a backbone atom as reference group in the first case and no reference group in the second case. The differences I found are as follows: When I use no reference group, the molecule center moves less along the Z axis than in case of a defined reference group. The reason I do bother about that fact is that I do not want my molecule to leave the box on one end due to pulling effects even though the box is more than 3 nm longer than the unfolded protein. Also, pullf.xvg shows quite similar values for the simulation without reference group whereas forces differ more if a reference group is used. (see attached files). Why is that so? Best wishes, Ilona Quoting Berk Hess g...@hotmail.com: Hi, Everything depends on what you want to accomplish, which you do not write. I don't see why you would want to look at single atoms. Since you pull on COM's, only the COM coordinates are relevant. If you want to look at single atoms, simply store them in the xtc file. If you have only two groups, there is no physical difference between the reference group and the first pull group. They are simply two groups between which the distance is calculated and the forces act. If you used an absolute reference, 0Z is the absolute reference coordinate, not the coordinate of a group. Berk Date: Tue, 23 Jun 2009 14:39:48 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: gmx-users@gromacs.org Subject: RE: [gmx-users] pullx.xvg Meaning of output? Dear Berk, Thanks for the quick reply. That leads me to my next questions: *I used the whole N and C residues for pulling. Is there any way of reconstructing the values for the single atoms? Or do you recommend only to pull N and C in the first place? *What does the reference group actually do? Can I simply leave it out? Does it influence pulling? What would be a good reference group? A random backbone atom from the middle of the protein? I'm looking forward to your reply. Thank you very much in advance. Best wishes, Ilona Quoting Berk Hess g...@hotmail.com: Hi, This is actually not (yet) documented. 0Z is the Z-coordinate of group 0. 1dZ is the the Z-coordinate of group 1 minus the one of group 0. Berk
Re: [gmx-users] use of LAN for parallel processing
akalabya bissoyi wrote: Thanks gromacs for you replay, can any body provide tutorial/standard protocol how to use of LAN for parallel processing. The canonical guide for doing installations of MPI versions of GROMACS can be found here http://oldwww.gromacs.org/content/view/19/32/ Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: How to freeze the atoms?
I do not see topology file in your archive. 2009/6/25 toby10222...@sina.com The input files for EM of the job are in the attachment. Thank you for your time! - 原始邮件 - 发件人：Vitaly V. Chaban vvcha...@gmail.com 收件人：toby10222...@sina.com, gmx-users@gromacs.org 主题：Re: 回复：Re: 回复：[gmx-users] Re: How to freeze the atoms? 日期：2009-6-24 19:10:19 It's difficult to say anything definite about your problem based on the provided information. If the effect is critical for your job you may send me all the input files of your system and hopefully I will try to look at them on these days. 2009/6/24 toby10222...@sina.com I checke the ndx file and the numbers of atoms in that file are the same as in the corresponding residues. The atoms only move in EM and they stay still during equilibrium process. I have not run MD yet. So I don't know whether the atoms will move or not during MD run. Thank you! - 原始邮件 - 发件人：Vitaly V. Chaban vvcha...@gmail.com 收件人：toby10222...@sina.com, gmx-users@gromacs.org 主题：Re: 回复：[gmx-users] Re: How to freeze the atoms? 日期：2009-6-24 13:00:20 I do not know such effect although work with the 'freeze' option for a number of years in many gromacs versions. Are you sure that the numbers of the atoms in your ndx file are the same as in the corresponding residues? I suggest that you should look for a problem there. Do the atoms move only when EM is performed or during MD run as well? - Vitaly 2009/6/24 toby10222...@sina.com Dear all The CNT itself does not move. Only C and O in carbonyl groups move and the distance of movement is not large. As I wrote, Each carbonyl group (C and O ) is considered as a residue named Car and the group name of carbonyl in the ndx file is Car, too. Is there anything wrong with the groups? Is it possible that the frozen atoms move a short distance due to the strong electrostatic forces. C in the CNT has no charge, while atoms in carbonyl groups take charges. Thank you for your time! - 原始邮件 - 发件人：Vitaly V. Chaban vvcha...@gmail.com 收件人：gmx-us...@gromacs.org 主题：[gmx-users] Re: How to freeze the atoms? 日期：2009-6-23 18:04:35 Dear all I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each carbonyl group is considered as a residue named Car and each carbon atom in the CNT is considered as a residue named Gr1. In the mdp file, the freezegrps are Gr1 and Car, and the freezedim are Y Y Y Y Y Y. Does it mean that all the C in the CNT and C and O in the carbonyl groups are fixed in three dimensions and they can not move in any direction. However, when I made the energy minimization, the coordinates of C and O in carbonyl groups changed. How can I really fix the atoms? Look forward for your suggestions! All the atoms which relate to your frozen groups should be non-movable during MD. the coordinates of C and O in carbonyl groups changed. Only ones of CHO changed? And the CNT itself is nonmovable? Check your groups please. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] angle
Dear gmxusers I want to calculate the angle between 2 alpha helix. One of the possibility to do, is g_bundle command. If I want to use g_bundle I have a problem to define the groups in the index file. On a basis of which criteria could I choose the 3 group in index file as input for g_bundle??? Before thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] angle
Morteza Khabiri wrote: Dear gmxusers I want to calculate the angle between 2 alpha helix. One of the possibility to do, is g_bundle command. If I want to use g_bundle I have a problem to define the groups in the index file. On a basis of which criteria could I choose the 3 group in index file as input for g_bundle??? Does the contents of g_bundle -h help? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] use of LAN for parallel processing
Hi Mark Do you know any site/paper/book which clearly discuss the use of other network paradigms (infiniband, myrinet, etc) to perform fair parallel MD simulations? Thanks! ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Mark Abraham escreveu: akalabya bissoyi wrote: Thanks gromacs for you replay, can any body provide tutorial/standard protocol how to use of LAN for parallel processing. The canonical guide for doing installations of MPI versions of GROMACS can be found here http://oldwww.gromacs.org/content/view/19/32/ Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] use of LAN for parallel processing
Alexandre Suman de Araujo wrote: Hi Mark Do you know any site/paper/book which clearly discuss the use of other network paradigms (infiniband, myrinet, etc) to perform fair parallel MD simulations? No. GROMACS will work over any network across which you can run MPI. For MD, you are likely to get what you pay for with that network. You can search the archives of gmx-users for some discussion here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] handling particle decomposition with distance restraints
The energy minimization went on without any problem on 4 processors but the problem occurs when I perform the MD run. Also, I did not get any error message with relevance to LINCS etc... JJ On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Yes my distance restraints are long because I am using FRET distances as distance restraints while performing MD simulations. Upon usage of this command mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro -pd I get the following error!! I did try giving yes after -pd but even then the same error message is repeated. Anything else printed to the screen or log file? LINCS warnings or anything else? Did energy minimization complete successfully? -Justin Back Off! I just backed up md.log to ./#md.log.9# Reading file pr.tpr, VERSION 4.0 (single precision) NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain NODEID=1 argc=13 NODEID=3 argc=13 [localhost:17514] *** Process received signal *** [localhost:17514] Signal: Segmentation fault (11) [localhost:17514] Signal code: Address not mapped (1) [localhost:17514] Failing at address: 0x134 [localhost:17514] [ 0] /lib64/libpthread.so.0 [0x38dec0f0f0] [localhost:17514] [ 1] /lib64/libc.so.6(memcpy+0x15b) [0x38de08432b] [localhost:17514] [ 2] /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(ompi_convertor_pack+0x152) [0x3886e45392] [localhost:17514] [ 3] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0x13d) [0x7f39dd118a4d] [localhost:17514] [ 4] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rndv+0x140) [0x7f39dd735230] [localhost:17514] [ 5] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x748) [0x7f39dd72e508] [localhost:17514] [ 6] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_split_bintree+0x91c) [0x7f39dc6f735c] [localhost:17514] [ 7] /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(MPI_Bcast+0x15c) [0x3886e4c40c] [localhost:17514] [ 8] mdrun_mpi(bcast_state+0x26c) [0x56d59c] [localhost:17514] [ 9] mdrun_mpi(mdrunner+0x1067) [0x42b807] [localhost:17514] [10] mdrun_mpi(main+0x3b4) [0x431c34] [localhost:17514] [11] /lib64/libc.so.6(__libc_start_main+0xe6) [0x38de01e576] [localhost:17514] [12] mdrun_mpi [0x413339] [localhost:17514] *** End of error message *** mpirun noticed that job rank 0 with PID 17514 on node localhost.localdomain exited on signal 11 (Segmentation fault). 3 additional processes aborted (not shown) On Wed, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: jayant james wrote: I just replaced the old gmx 4.0 version with the 4.0.5 version and still the same problem NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) Well, does it work with -pd? It looks like your distance restraints are indeed quite long, so this looks like it is your only option. -Justin WARNING: Can not write distance restraint data to energy file with domain decomposition On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: jayant james wrote: Hi! I am performing an mpi MD (on a quad core system) run with distance restraints. When I execute this command below without position restraints the MD run is distributed over 4 nodes perfectly well. But when I incorporate the distance restraints I hit a road block mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro I get this error message (below). My pr.mdp and distance restraints files are given below the error message . * Question.* How do I handle this sitation? Do I increase the long range cut off in the pr.mdp file? If you see my distance restraints file, my upper range of distances are close to 9nm!! Upgrade to the latest version (4.0.5), since there have been numerous improvements to domain decomposition throughout the development of version 4.0. -Justin Please guide. Thanks JJ -- Back Off! I just backed up md.log to ./#md.log.6# Reading file pr.tpr, VERSION 4.0 (single precision) NOTE: atoms involved in distance
[gmx-users] angle
Dear gmxusers I want to calculate the angle between 2 alpha helix. One of the possibility to do, is g_bundle command. If I want to use g_bundle I have a problem to define the groups in the index file. On a basis of which criteria could I choose the 3 group in index file as input for g_bundle??? Before thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] handling particle decomposition with distance restraints
Why not use the pull code? If you haev to use distance restraints, then try LAM mpi with your pd run. We had similar error messages with vanilla .mdp files using openmpi with large and complex systems that went away when we switched to LAM MPI. Our problems disappeared in gmx 4 so we went back to openmpi for all systems as that mdrun_mpi version is faster in our hands. I admit, there is no good reason why LAM would work and openMPI would not, but I have seen it happen before so it's worth a shot. -- original message-- The energy minimization went on without any problem on 4 processors but the problem occurs when I perform the MD run. Also, I did not get any error message with relevance to LINCS etc... JJ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] handling particle decomposition with distance restraints
Let me re-emphasize that the pull code may be a good solution for you. As per your request, I currently use the following without any problems: fftw 3.1.2 gromacs 3.3.1 or 4.0.4 openmpi 1.2.6 Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I posted here: http://lists.gromacs.org/pipermail/gmx-users/2009-March/040844.html To be clear, I have never experienced any openmpi-based problems with any version of gromacs 4 and openmpi 1.2.6. I posted the original notice of our problems with openmpi (1.2.1) that were solved by using lam here. http://www.mail-archive.com/gmx-users@gromacs.org/msg08257.html Chris jayant james wrote: Hi! thanks for your mail. Could you please share what OS and versions of fftw, openmpi and gmx you are currently using. Thanks you JJ On Thu, Jun 25, 2009 at 12:28 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Why not use the pull code? If you haev to use distance restraints, then try LAM mpi with your pd run. We had similar error messages with vanilla .mdp files using openmpi with large and complex systems that went away when we switched to LAM MPI. Our problems disappeared in gmx 4 so we went back to openmpi for all systems as that mdrun_mpi version is faster in our hands. I admit, there is no good reason why LAM would work and openMPI would not, but I have seen it happen before so it's worth a shot. -- original message-- The energy minimization went on without any problem on 4 processors but the problem occurs when I perform the MD run. Also, I did not get any error message with relevance to LINCS etc... JJ ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] handling particle decomposition with distance restraints
We are running SUSE Linux It's best to keep all of this on the mailing list in case it becomes useful to somebody else. jayant james wrote: Hi! thanks for your mail. I have never used pull code before and so I am a bit apprehensive but I do accept your suggestion and I am working on that. By the wat what is the OS that you are using? Is it Suse or Fedora? Thanks Jayant James On Thu, Jun 25, 2009 at 4:31 PM, Chris Neale chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Let me re-emphasize that the pull code may be a good solution for you. As per your request, I currently use the following without any problems: fftw 3.1.2 gromacs 3.3.1 or 4.0.4 openmpi 1.2.6 Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I posted here: http://lists.gromacs.org/pipermail/gmx-users/2009-March/040844.html To be clear, I have never experienced any openmpi-based problems with any version of gromacs 4 and openmpi 1.2.6. I posted the original notice of our problems with openmpi (1.2.1) that were solved by using lam here. http://www.mail-archive.com/gmx-users@gromacs.org/msg08257.html Chris jayant james wrote: Hi! thanks for your mail. Could you please share what OS and versions of fftw, openmpi and gmx you are currently using. Thanks you JJ On Thu, Jun 25, 2009 at 12:28 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Why not use the pull code? If you haev to use distance restraints, then try LAM mpi with your pd run. We had similar error messages with vanilla .mdp files using openmpi with large and complex systems that went away when we switched to LAM MPI. Our problems disappeared in gmx 4 so we went back to openmpi for all systems as that mdrun_mpi version is faster in our hands. I admit, there is no good reason why LAM would work and openMPI would not, but I have seen it happen before so it's worth a shot. -- original message-- The energy minimization went on without any problem on 4 processors but the problem occurs when I perform the MD run. Also, I did not get any error message with relevance to LINCS etc... JJ ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
