Re: [gmx-users] eigenvalues
Hi, Well, the trace of the covariance matrix (thus the sum of the eigenvectors), should say something about overall flexibility. In that case, the observation that the protein with ligand seems more flexible than without is not completely incorrect. However, the question arises regarding the nature of flexibility. Unless you have a perfectly equilibrated system, the assessment of flexibility using covariance analysis also includes a conformational drift. You can check equilibration by looking at the cosine content of the pc's. Another thing that matters is the structure you use for fitting, which also influences results from RMSD/RMSF. I don't know how large your system is, but you might try and do the covariance analysis on the last 10 ns. For very large systems, equilibration will likely take even longer. Hope it helps, Tsjerk On Thu, Jan 8, 2009 at 12:33 PM, Xavier Periole x.peri...@rug.nl wrote: On Thu, 8 Jan 2009 16:31:01 +0530 (IST) sanja...@iitb.ac.in wrote: dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenvector, when i compared eigenvalues i find that protein_withligands has high values in compare to protein alone, but from literature protein alone is more flexible structure and after ligand binding it changes in to more rigid structure. primary analysis like RMSD, RMSF calculation showing high values for protein alone in compare to protien_withligands. i think i should also get higher eigenvalue for protein alone.. is any thing wrong with my trajectory. i had used same mdp file for both simulation. i am sending values of Ist 10 eigenvector for make my question more clear. any suggestion is appreciable The eigenvalues alone do not mean much. They probably do not correspond to the same eigenvectors. You have to compare the eigenvectors from the two simulations. This is possible using a RMSIP (root mean square inner product). You'll find the definition and more details in papers from Amadei and Ceruso. hints: Amadei et al., 1999; Ceruso et al., 1999a,b, 2003; Merlino et al., 2003; Roccatano et al., 2003 Best, XAvier. protein-withligands 1 1.48497 2 0.674994 3 0.410547 4 0.279636 5 0.237182 6 0.213209 7 0.158359 8 0.140052 9 0.126227 10 0.113618 protein alone 1 0.526848 2 0.351471 3 0.267247 4 0.248945 5 0.222829 6 0.204475 7 0.158441 8 0.12583 9 0.0970591 10 0.0923962 thanks sanjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Onw question about rlist rvdw rcoulomb and nstlist
For treatments that require a non-zero buffer length, like shift and switch, you do this by setting rlist larger than rcoulomb. Coulomb should be fine with PME + straight cutoff and the difference for LJ between nstlist=1 and nstlist=10 I expect will be negligible for a 2fs timestep. Note that I have never tried shifting or switching in gromacs, but charmm-like behaviour here seems 100% possible in gromacs. Here is some stuff from the manual: The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rcoulomb to accommodate for the size of charge groups and diffusion between neighbor list updates. The neighbor search cut-off rlist should be 0.1 to 0.3 nm larger than rvdw to accommodate for the size of charge groups and diffusion between neighbor list updates. So yes, it is not possible to use a cutoff for coulombic and LJ while having nstlist1 and obtaining results that are identical to those that would be obtained with nstlist=1 (or with sufficient 'buffer'). If you really must do this then set nstlist=1. Chris. -- original message -- Usually when we do neighbour searching we should give three parameters: cut-off distance, buffer length and the frequency of the neighbour list updating. But in Gromacs *.mdp file it's just required to give rlist,nstlist, rvdw and rcoumlomb. Where is the buffer length of neighbour searching in Gromacs? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eigenvalues
Hi. As far as I know, PCA analysis breaks your total motion in system, or rather decouples it into respective motions. And by the eigenvectors and the corresponding eigenvalues it means that this 1st vector or the 2nd vector contributes this percent of the total motion. It is system-dependent. Is this really related to the difference in the degrees of freedom of two different systems (that I am a bit skeptic about) with which you are confusing it now. If I am missing something here, then anyone please correct me. Regards, Monika On Thu, Jan 8, 2009 at 4:31 PM, sanja...@iitb.ac.in wrote: dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenvector, when i compared eigenvalues i find that protein_withligands has high values in compare to protein alone, but from literature protein alone is more flexible structure and after ligand binding it changes in to more rigid structure. primary analysis like RMSD, RMSF calculation showing high values for protein alone in compare to protien_withligands. i think i should also get higher eigenvalue for protein alone.. is any thing wrong with my trajectory. i had used same mdp file for both simulation. i am sending values of Ist 10 eigenvector for make my question more clear. any suggestion is appreciable protein-withligands 1 1.48497 2 0.674994 3 0.410547 4 0.279636 5 0.237182 6 0.213209 7 0.158359 8 0.140052 9 0.126227 10 0.113618 protein alone 1 0.526848 2 0.351471 3 0.267247 4 0.248945 5 0.222829 6 0.204475 7 0.158441 8 0.12583 9 0.0970591 10 0.0923962 thanks sanjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Dear gmx user, I want to simulate one cytochrome protein inside the water box. Unfortunately in the stage of pdb2gmx I faced with the following error: Residue 'HEME' not found in residue topology database How could I involve heme group? Before thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eigenvalues
Hi Monika, As far as I know, PCA analysis breaks your total motion in system, or rather decouples it into respective motions. Well, formally, PCA tries to provide an explanation of the total variance in the system, in terms of a set of new, linearly unrelated variables. And by the eigenvectors and the corresponding eigenvalues it means that this 1st vector or the 2nd vector contributes this percent of the total motion. Variance is not motion. I can be running small circles, being very motile, but having a small variance. I can also steadily go from one place to another. Though I don't need to be very active, there'll be a large variance in my position. So the variance is more linked to the range of conformations and the extent of the conformational space accessible than of the motility. Only if you can be sure that there's no trend - no going from one place to the other - but periodic motions (running circles), you can say the variance is a measure of motility. It is system-dependent. Is this really related to the difference in the degrees of freedom of two different systems (that I am a bit skeptic about) with which you are confusing it now. No, not of different systems, but of the same (very similar) system(s) under different conditions, each in equilibrium, yes. Cheers, Tsjerk -- 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 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] eigenvalues
Hi Tsjerk, Thank you very much for correcting me. And yes that is variance, not the literal motion. Regards, Monika On Fri, Jan 9, 2009 at 6:50 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Monika, As far as I know, PCA analysis breaks your total motion in system, or rather decouples it into respective motions. Well, formally, PCA tries to provide an explanation of the total variance in the system, in terms of a set of new, linearly unrelated variables. And by the eigenvectors and the corresponding eigenvalues it means that this 1st vector or the 2nd vector contributes this percent of the total motion. Variance is not motion. I can be running small circles, being very motile, but having a small variance. I can also steadily go from one place to another. Though I don't need to be very active, there'll be a large variance in my position. So the variance is more linked to the range of conformations and the extent of the conformational space accessible than of the motility. Only if you can be sure that there's no trend - no going from one place to the other - but periodic motions (running circles), you can say the variance is a measure of motility. It is system-dependent. Is this really related to the difference in the degrees of freedom of two different systems (that I am a bit skeptic about) with which you are confusing it now. No, not of different systems, but of the same (very similar) system(s) under different conditions, each in equilibrium, yes. Cheers, Tsjerk -- 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 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Equilibrating systems of rigid molecules
Hi, is it possible to simulate rigid molecules with GROMACS? It seems that the run option constraints = all-angles does this, but using it requires SHAKE, which cannot be used in energy minimization. How can one generate suitable starting configurations of rigid molecules? At least using a configuration minimized without any constraints seems to crash in the first step since SHAKE cannot satisfy the constraints in the allowed number of steps.. Also: what is the reference used for the constraints? Is it the force field parameters, or the starting configuration..? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Equilibrating systems of rigid molecules
Jussi Lehtola wrote: Hi, is it possible to simulate rigid molecules with GROMACS? It seems that the run option constraints = all-angles does this, but using it requires SHAKE, which cannot be used in energy minimization. How can one generate suitable starting configurations of rigid molecules? At least using a configuration minimized without any constraints seems to crash in the first step since SHAKE cannot satisfy the constraints in the allowed number of steps.. Also: what is the reference used for the constraints? Is it the force field parameters, or the starting configuration..? Unfortunately this is not possible. With constraints = all-angles you still have flexible dihedrals. You can also use all-angles with LINCS if you increase the iteration count (lincs-iter). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS warning
Hi! I am getting a message in the MD log file as below with respect ro LINCS mentioning deviations. I have constrained all bonds but this problem seems to pertain to a water molecule. Please suggest a way to oversome this issue. Thanks Jayant James Initializing LINear Constraint Solver number of constraints is 4539 average number of constraints coupled to one constraint is 2.9 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.048807 517 518 0.006284 After LINCS 0.000551 520 522 0.000113 Going to use C-settle (72211 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074 rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.064202 1746 1747 0.008456 After LINCS 0.000134 2867 2869 0.18 Started mdrun on node 0 Fri Jan 9 12:43:22 2009 Initial temperature: 299.944 K Step Time Lambda 0 0.0 0.0 Grid: 13 x 20 x 22 cells Configuring nonbonded kernels... Testing x86_64 SSE support... present. Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.015569 675 676 0.001354 After LINCS 0.80 520 522 0.14 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 2.96794e+03 2.64964e+03 9.36791e+02 1.39165e+03 4.77210e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest. 6.48697e+05 -9.38928e+03 -4.00822e+06 -4.30837e+05 2.74831e+03 D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature 1.27022e+01 -3.74134e+06 5.53033e+05 -3.18830e+06 2.99966e+02 Pressure (bar) -2.82027e+03 Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Step Time Lambda 5000 5.0 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.014423 4388 4389 0.001377 After LINCS 0.26 3409 3410 0.06 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.22704e+03 3.55030e+03 2.16248e+03 1.62198e+03 4.75481e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest. 5.11526e+05 -9.27329e+03 -3.36888e+06 -4.42423e+05 3.30945e+02 D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature 4.61447e+00 -3.24661e+06 5.52683e+05 -2.69393e+06 2.99776e+02 Pressure (bar) 2.28435e+01 Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Step Time Lambda 1 10.0 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.016397 3336 3337 0.001453 After LINCS 0.25 2689 2691 0.06 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.09757e+03 3.64033e+03 2.11140e+03 1.63821e+03 4.76074e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Dis. Rest. 5.13273e+05 -9.28148e+03 -3.37251e+06 -4.42402e+05 2.78608e+02 D. R. Viol. (nm) Potential Kinetic En. Total Energy Temperature 4.20109e+00 -3.24855e+06 5.53775e+05 -2.69477e+06 3.00369e+02 Pressure (bar) 1.19419e+02 Grid: 13 x 21 x 22 cells Grid: 13 x 21 x 23 cells Step Time Lambda 15000 15.0 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.016405 2451 2452 0.001466 After LINCS 0.30 520 522 0.06 -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Best performace with 0 core for PME calcuation
Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system is 9.6x9.6x10.1 nm^3. I'm using the following parameters: * nstlist = 10 * rlist = 1 * Coulombtype = PME * rcoulomb = 1 * fourier spacing = 0.12 * vdwtype = Cutoff * rvdw = 1 The cluster itself has got 2 procs/node connected by Ethernet 100 MB/s. I'm using mpiexec to run Gromacs. When I use -npme 2 -ddorder interleave, I get: ncorePerf (ns/day)PME (%) 10,000 20,000 30,000 41,3528 51,8431 62,0827 82,0921 102,2517 122,0215 142,2013 162,0411 182,1810 202,299 So, above 6-8 cores, the PP nodes are spending too much time waiting for the PME nodes and the perf forms a plateau. When I use -npme 0, I get: ncorePerf (ns/day)PME (%) 10,4333 20,9234 31,3435 41,6936 52,1733 62,5632 83,2433 103,8434 124,3435 145,0532 165,4734 185,5437 206,1336 I obtain much better performances when there is no PME nodes, while I was expecting the opposite. Does someone have an explanation for that? Does that means domain decomposition is useless below a certain real space cutoff? I'm quite confused. Thanks, Nicolas begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:nsa...@ucalgary.ca title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Best performace with 0 core for PME calcuation
Nicolas a écrit : Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system is 9.6x9.6x10.1 nm^3. I'm using the following parameters: * nstlist = 10 * rlist = 1 * Coulombtype = PME * rcoulomb = 1 * fourier spacing = 0.12 * vdwtype = Cutoff * rvdw = 1 The cluster itself has got 2 procs/node connected by Ethernet 100 MB/s. I'm using mpiexec to run Gromacs. When I use -npme 2 -ddorder interleave, I get: Little mistake: I used the wrong cluster specifications. There is 4 cores per nodes and they communicate with Infiniband. ncorePerf (ns/day)PME (%) 10,000 20,000 30,000 41,3528 51,8431 62,0827 82,0921 102,2517 122,0215 142,2013 162,0411 182,1810 202,299 So, above 6-8 cores, the PP nodes are spending too much time waiting for the PME nodes and the perf forms a plateau. When I use -npme 0, I get: ncorePerf (ns/day)PME (%) 10,4333 20,9234 31,3435 41,6936 52,1733 62,5632 83,2433 103,8434 124,3435 145,0532 165,4734 185,5437 206,1336 I obtain much better performances when there is no PME nodes, while I was expecting the opposite. Does someone have an explanation for that? Does that means domain decomposition is useless below a certain real space cutoff? I'm quite confused. Thanks, Nicolas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:nsa...@ucalgary.ca title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Best performace with 0 core for PME calcuation
Nicolas wrote: Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system is 9.6x9.6x10.1 nm^3. I'm using the following parameters: * nstlist = 10 * rlist = 1 * Coulombtype = PME * rcoulomb = 1 * fourier spacing = 0.12 * vdwtype = Cutoff * rvdw = 1 The cluster itself has got 2 procs/node connected by Ethernet 100 MB/s. Ethernet and Gigabit ethernet are not fast enough to get reasonable scaling. There've been quite a few posts on this topic in the last six months. Hmm I see you've corrected your post to refer to Infiniband with four cores/node. That should be reasonable, I understand (but search the archive). You should also check that your benchmark calculation is long enough that you are measuring a simulation time that isn't being dominated by setup costs. Some years ago a non-MD sysadmin complained of poor scaling when he was testing over 10 or so MD steps! I'm using mpiexec to run Gromacs. When I use -npme 2 -ddorder interleave, I get: ncorePerf (ns/day)PME (%) 10,000 20,000 30,000 41,3528 51,8431 62,0827 82,0921 102,2517 122,0215 142,2013 162,0411 182,1810 202,299 So, above 6-8 cores, the PP nodes are spending too much time waiting for the PME nodes and the perf forms a plateau. That's not surprising - the heuristic is that about a third to a quarter of the cores want to be PME-only nodes. Of course, that depends on the relative size of the real- and reciprocal-space parts of the calculation. When I use -npme 0, I get: ncorePerf (ns/day)PME (%) 10,4333 20,9234 31,3435 41,6936 52,1733 62,5632 83,2433 103,8434 124,3435 145,0532 165,4734 185,5437 206,1336 I obtain much better performances when there is no PME nodes, while I was expecting the opposite. Does someone have an explanation for that? Does that means domain decomposition is useless below a certain real space cutoff? I'm quite confused. The relevant observations are for 4,5,6 and 8, for which shared-duty is out-performing -npme 2. I think your observations support the conclusion that your network hardware is more limiting for PME-only nodes than shared-duty nodes. They don't support the conclusion that DD is useless, since you haven't compared with PD. You can play with the PME parameters to shift more load into the real-space part - IIRC Carsten suggested a heuristic a few months back. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] re : heme group
hi, heme group is not an amino acid, pdb2gmx only support the amino acids because .itp and .dat file in gromacs have only information about protein atoms not for other. so u just cut the co-ordinate of heme group from your pdb file save it in other pdb file and give input for Prodrg software it will return u co-ordinate of heme group in gromacs compatible format. u do pdb2gmx on only protein part and add both output file(pdb2gmx.gro and prodrg .gro)and proceed next step. u should read online John E. Kerrigan GROMACS Tutorial for Drug – Enzyme Complex. it will help u more. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf sanjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] eigenvalues
Hi Tsjerk, thanks actually my protein is quite larg (509 aa).i had divided my trajectory in different part and according to your suggestion i calculated cosine-content for all, and find that trajectory from 5to15 ns and 18to25ns having cosine value very less about 0.03 in both cases(with and without ligands), while other combination showing higher values (0.6).so i think my system is Ist converges around 5ns and maintaining it up to 15 ns after that it may be few conformational fluctuation occurring and finally it get stabilized from 18to15ns.may that part 15to18ns trajectory is transition period between to conformational fluctuation. i have also calculated temp. and pressure during whole simulation and i find that it is exact Gaussian between 5to25ns.so my confusion is whether i take my trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25, but 5to25 showing value of cosine 0.6. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
