Re: [gmx-users] Simulation time losses with REMD
1 102.249 34.9 1.8 > 7405c6920 > < Total 16108.520 2087.5 100.0 > --- > > Total 15761.363 1968.8 100.0 > > Here 102 s becomes 417 s despite factoring out 60 s for REMD. So the > time spent doing the exchange is just noticeable, but quite a bit less > than the observed increase in total time. > > For the lowest replica in parallel: > > 8481,8496c7971,7985 > < Domain decomp. 8 25010 152.338 52.1 1.8 > < DD comm. load 8 242261.0850.4 0.0 > < DD comm. bounds8 242194.1671.4 0.0 > < Vsite constr. 8 250001 62.857 21.5 0.8 > < Comm. coord. 8 250001 132.068 45.1 1.6 > < Neighbor search8 25010 367.001 125.4 4.4 > < Force 8 250001 3446.528 1177.841.2 > < Wait + Comm. F 8 250001 252.245 86.2 3.0 > < PME mesh 8 250001 2113.009 722.125.3 > < Vsite spread 8 52 102.749 35.1 1.2 > < Write traj.8 11.2060.4 0.0 > < Update 8 250001 85.793 29.3 1.0 > < Constraints8 250001 464.294 158.7 5.5 > < Comm. energies 8 250002 73.343 25.1 0.9 > < REMD 8100 162.661 55.6 1.9 > < Rest 8 945.642 323.211.3 > --- > > Domain decomp. 8 25001 146.561 50.1 2.0 > > DD comm. load 8 229430.9890.3 0.0 > > DD comm. bounds8 229013.7681.3 0.1 > > Vsite constr. 8 250001 64.035 21.9 0.9 > > Comm. coord. 8 250001 124.487 42.5 1.7 > > Neighbor search8 25001 367.342 125.5 5.0 > > Force 8 250001 3443.161 1176.746.9 > > Wait + Comm. F 8 250001 237.697 81.2 3.2 > > PME mesh 8 250001 2119.205 724.228.9 > > Vsite spread 8 52 95.092 32.5 1.3 > > Write traj.8 10.9200.3 0.0 > > Update 8 250001 85.529 29.2 1.2 > > Constraints8 250001 391.469 133.8 5.3 > > Comm. energies 8 250002 120.291 41.1 1.6 > > Rest 8 139.127 47.5 1.9 > 8498c7987 > < Total 88366.984 2859.3 100.0 > --- > > Total 87339.674 2508.3 100.0 > > Again REMD exchanges are only a small fraction of the increase (139 s to > 946 s despite 163 s accounted for). > > Does anyone have a theory on what could be causing this? > > Mark > No theory, but some more data. I've been running REMD on a fairly large system, with 48 replicas between 300K and 400K. I have runs using Gromacs 4.5.3 and 2, 4 or 16 processors per replica. As a general statement, it all seems to scale fine, and no great delays from the RE. However, I did do some quick timing checks for the 2 procs per replica case. I simply hacked in a few timing statements, so nothing so polished as your hack :) An average MD step takes about 0.3 s. The time spent in the replica exchange attempt (which I took to be the time in the call to replica_exchange() from md.c) was around 0.003 s, i.e. about 1% for a RE cycle. Given that I only attempt an exchange every 1000 cycles, I took this to be negligible. The only odd thing I saw was that on a RE cycle it appears to spend 0.6s in do_force() which is twice the average MD step time. I didn't print this out for non-RE cycles, so no sanity check I am afraid. For time lost in REMD, I guess the issue is when the replicas get synchronised. There seems to be an MPI_Allreduce called as part of get_replica_exchange() (when it collects the potential energies) which is within my timings, but I am not sure if there is anything else. Sorry that these figures are a bit rough and ready, but they do seem to support your finding that the calls to REMD aren't to blame. Cheers Martyn -- *** * * * Dr. Martyn Winn * *
Re: [gmx-users] b-factor
On Wed, 2010-06-30 at 13:07 +0200, Erik Marklund wrote: > leila karami skrev: > > Hi all > > > > pdb file for my protein was obtained by solution NMR. this file is as > > follows : > > > > ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 > > ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 > > ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 > > ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00 > > ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00 > > ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00 > > ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00 > > ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00 > > > > pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq > > command is as follws : > > > > ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65 > > ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41 > > ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09 > > ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27 > > ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51 > > ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99 > > ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70 > > ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64 > > > > so can I compare experimental B-factor with that calculated from MD? > > > > any help will highly appreciated. > I'm currently calculating b-factors too, and there may be two things > that you must think about. One is, as I understand it, that the b-factor > in x-ray scattering experiments is unaffected by motions in the > scattering directoion, effectively reducing the observerd mds of the > atoms so that B = pi^2 * 8 * msd_p, where msd_p is only the motions > perpendicular to the scattering direciton. Another thing to consider is > wether isotropic b-factors is suitable in your case. > > Erik I don't think the scattering direction is a significant factor. Each atom occurs in multiple asymmetric units, and so in multiple orientations in the crystal, depending on the spacegroup. In any case, the diffraction intensities are averaged over multiple observations, taken at different crystal orientations with respect to the beam. More serious is that the B factor soaks up many sources of uncertainty: molecular motion (e.g. from crystal phonons), internal motions, static disorder, errors in the data, effects of partial occupancy, etc. In my experience, the rmsd calculated from a B factor is much larger than that calculated from MD, and quantitative comparison is impossible. But you may well be able to see qualitative similarities. Note also that you are comparing the molecule in solution with the molecule in the crystal, and there will certainly be differences near crystal contacts. There is no B factor for NMR structures. The closest equivalent is to look at the variation between MODELs in a PDB entry. Cheers Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** -- 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] analyzing beta factor
Ah yes, of course. I keep forgetting these strange units ;-) m On Wed, 2009-02-04 at 11:16 +0100, David van der Spoel wrote: > Martyn Winn wrote: > > The factor is 8 * pi^2 > > The 100 comes from nm to Angstrom. > > > The factor 1/3 arises when you take the trace of an anisotropic > > displacement parameter. > > But I believe g_rmsf will do this conversion anyway with options -oq or > > -ox (I've not tested this, just read the documentation) > Only when writing to a pdb file. > > > > > Cheers > > Martyn > > > > On Wed, 2009-02-04 at 09:05 +0100, David van der Spoel wrote: > >> özge kül wrote: > >>> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Alif M Latif > >>> Sent: 02 May 2008 09:42 > >>> To: gmx-users@gromacs.org > >>> Subject: [gmx-users] Plotting B-factor > >>> > >>> Dear GROMACS users and developers, > >>> > >>> I want to plot B-factor of a protein structure against residue. How can I > >>> do > >>> that?. Using option -oq in g_rmsf only produce bfac.pdb which is in .pdb > >>> file > >>> and assigned at each atom. Is there another way I can get the plot > >>> B-factor vs > >>> residue?. Any link to example or tutorial will be very helpful. > >>> Comments and Suggestions are greatly appreciated. Thank you. > >> Take the g_rmsf -res output, square it and multiply it by (IIRC) 800 > >> pi^2/3 (you can do all this in xmgrace). Check the factor. > >>> Muhammad Alif Mohammad Latif > >>> Department of Chemistry > >>> Faculty of Science > >>> Universiti Putra Malaysia > >>> 43400 UPM Serdang, Selangor > >>> MALAYSIA > >>> > >>> > >>> > >>> --- On *Wed, 2/4/09, David van der Spoel //* wrote: > >>> > >>> From: David van der Spoel > >>> Subject: Re: [gmx-users] analyzing beta factor > >>> To: "Discussion list for GROMACS users" > >>> Date: Wednesday, February 4, 2009, 2:16 AM > >>> > >>> özge kül wrote: > >>> > Hi users, > >>> > > >>> > I want to plot beta factor versus residue number plot at the > >>> analyzing > >>> part.I read manual and search in the web but I could not find a > >>> reasonable > >>> result for this plot.I wonder if anybody know about it. > >>> > > >>> What is the beta factor? > >>> > >>> > >>> > Thank you, > >>> > Özge > >>> > > >>> > > >>> > > >>> > > >>> > >>> > > >>> > ___ > >>> > 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 > >>> > >>> > >>> -- 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.se sp...@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 > >>> > >>> > >>> > >>> ---
Re: [gmx-users] monoclinic super cell
For a start, the 'P 1 21 1' on the CRYST1 line is a different spacegroup from 'P 21/b'. The former implies Z=2. In principle, it should be straightforward to generate it yourself by applying the 4 symmetry operators to your starting coordinates. You then need to know whether 'P 21/b' is 'P 1 1 21/b' or 'P 21/b 1 1' Cheers Martyn On Tue, 2009-02-03 at 21:35 -0800, farzaneh fatahi wrote: > Hi, > I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. > I have found a PDB of CA5 (PO4)3 (OH) in internet , whitch consits of 22 > atoms. > the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) > it means to generate the super cell of HAP i have to feed editconf with the > appropriate CRYST1 record in PDB file. > > CRYST1 9.42 18.866.8890.00 120.00 90.00 P 1 21 1 4 > > according to CRYST1 record: because of Z value and space group i should get > a .gro > file of the whol 88 atoms but editconf gives me only a .gro file with 22 atom. > am i on the right way to generate the super cell with 88 atoms. > I appreciate your help! > > > > ___ > 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 -- ******* * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** ___ 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] analyzing beta factor
The factor is 8 * pi^2 The factor 1/3 arises when you take the trace of an anisotropic displacement parameter. But I believe g_rmsf will do this conversion anyway with options -oq or -ox (I've not tested this, just read the documentation) Cheers Martyn On Wed, 2009-02-04 at 09:05 +0100, David van der Spoel wrote: > özge kül wrote: > > From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Alif M Latif > > Sent: 02 May 2008 09:42 > > To: gmx-users@gromacs.org > > Subject: [gmx-users] Plotting B-factor > > > > Dear GROMACS users and developers, > > > > I want to plot B-factor of a protein structure against residue. How can I > > do > > that?. Using option -oq in g_rmsf only produce bfac.pdb which is in .pdb > > file > > and assigned at each atom. Is there another way I can get the plot B-factor > > vs > > residue?. Any link to example or tutorial will be very helpful. > > Comments and Suggestions are greatly appreciated. Thank you. > Take the g_rmsf -res output, square it and multiply it by (IIRC) 800 > pi^2/3 (you can do all this in xmgrace). Check the factor. > > > > Muhammad Alif Mohammad Latif > > Department of Chemistry > > Faculty of Science > > Universiti Putra Malaysia > > 43400 UPM Serdang, Selangor > > MALAYSIA > > > > > > > > --- On *Wed, 2/4/09, David van der Spoel //* wrote: > > > > From: David van der Spoel > > Subject: Re: [gmx-users] analyzing beta factor > > To: "Discussion list for GROMACS users" > > Date: Wednesday, February 4, 2009, 2:16 AM > > > > özge kül wrote: > > > Hi users, > > > > > > I want to plot beta factor versus residue number plot at the analyzing > > part.I read manual and search in the web but I could not find a > > reasonable > > result for this plot.I wonder if anybody know about it. > > > > > What is the beta factor? > > > > > > > Thank you, > > > Özge > > > > > > > > > > > > > > > > > > > > ___ > > > 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 > > > > > > -- 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 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 > > -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** ___ 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] infelicity in installation of 4.0.2
Hi I hadn't source'd the GMXRC file, but that doesn't seem to help. But then I noticed that it ran fine in another terminal window. After a bit of experimentation, it seems to be to do with the length of PATH. In the first terminal, PATH is about 2000 characters long (don't ask ;-) Going to the second terminal where it worked, if I increase the PATH variable by adding /usr/local/gromacs/bin lots of times, I can make that crash too. A bit of grepping in the source code, I notice that gmxlib/futil.c has a few hard limits like char system_path[512] (it seems to strcat onto system_path without checking the length ??). Might this be the problem? For the record: [EMAIL PROTECTED]:~/gromacs/test_installation$ ldd /usr/local/gromacs/bin/editconf linux-vdso.so.1 => (0x7fff2abfc000) libgmxana.so.5 => /usr/local/gromacs/lib/libgmxana.so.5 (0x7f072254a000) libmd.so.5 => /usr/local/gromacs/lib/libmd.so.5 (0x7f0722258000) libgmx.so.5 => /usr/local/gromacs/lib/libgmx.so.5 (0x7f0721db4000) libxml2.so.2 => /usr/lib/libxml2.so.2 (0x7f0721a6d000) libnsl.so.1 => /lib/libnsl.so.1 (0x7f0721854000) libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x7f072159a000) libm.so.6 => /lib/libm.so.6 (0x7f0721319000) libSM.so.6 => /usr/lib/libSM.so.6 (0x7f072000) libICE.so.6 => /usr/lib/libICE.so.6 (0x7f0720ef6000) libX11.so.6 => /usr/lib/libX11.so.6 (0x7f0720bf3000) libc.so.6 => /lib/libc.so.6 (0x7f0720891000) libdl.so.2 => /lib/libdl.so.2 (0x7f072068d000) libz.so.1 => /usr/lib/libz.so.1 (0x7f0720476000) libpthread.so.0 => /lib/libpthread.so.0 (0x7f072025a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x7f0720059000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x7f071fe3e000) /lib64/ld-linux-x86-64.so.2 (0x7f07228d9000) libXau.so.6 => /usr/lib/libXau.so.6 (0x7f071fc3c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x7f071fa37000) Cheers Martyn On Tue, 2008-12-02 at 13:52 +0100, Florian Haberl wrote: > Hi, > > On Tuesday, 2. December 2008, Martyn Winn wrote: > > Hi all, > > > > I've compiled 4.0.2 from source on an EM64T machine running Ubuntu, > > using ./configure --enable-shared > > With all executables I've tried, I find: > > > > [EMAIL PROTECTED]:~/gromacs/test_installation$ editconf > > > > :-) G R O M A C S (-: > > > > *** stack smashing detected ***: editconf terminated > > Segmentation fault > > [EMAIL PROTECTED]:~/gromacs/test_installation$ which editconf > > /usr/local/gromacs/bin/editconf > > [EMAIL PROTECTED]:~/gromacs/test_installation$ > > /usr/local/gromacs/bin/editconf > > > > :-) G R O M A C S (-: > > > > Good ROcking Metal Altar for Chronical Sinners > > > > :-) VERSION 4.0.2 (-: > > > > i.e. it only runs fine if I specify the full path. Searching the > > archives, I found that this was reported in April 07, with a reply that > > it will be fixed in 3.3.2 > > > > Nothing more recent came up, but apologies if I missed it. > > can you paste the output of ldd $your_executable? > > Have you sourced the GMXRC file? > > > Greetings, > > Florian > > -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED]* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] infelicity in installation of 4.0.2
Hi all, I've compiled 4.0.2 from source on an EM64T machine running Ubuntu, using ./configure --enable-shared With all executables I've tried, I find: [EMAIL PROTECTED]:~/gromacs/test_installation$ editconf :-) G R O M A C S (-: *** stack smashing detected ***: editconf terminated Segmentation fault [EMAIL PROTECTED]:~/gromacs/test_installation$ which editconf /usr/local/gromacs/bin/editconf [EMAIL PROTECTED]:~/gromacs/test_installation$ /usr/local/gromacs/bin/editconf :-) G R O M A C S (-: Good ROcking Metal Altar for Chronical Sinners :-) VERSION 4.0.2 (-: i.e. it only runs fine if I specify the full path. Searching the archives, I found that this was reported in April 07, with a reply that it will be fixed in 3.3.2 Nothing more recent came up, but apologies if I missed it. Cheers Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED]* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
