[gmx-users] query about topolgen.pl
Hi Can any body please tell me how to install and execute topolgen.pl script in linux for generationf topology file. It is not given in the Readme file. 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] query regarding .top file
Hello I have generated .top file for an ligand with the mktop programm for OPLSAA force field , how do I include this .top file for the ligand along with that my protein in the gromacs run? Subarna Looking for local information? Find it on Yahoo! Local http://in.local.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] Re: openmm
Dear Mark, Thanks. I reread those file carefully and noticed the only implicit solvent. Sorry for that. I am building my test case here to see by myself how fast it can be. Alan On Sat, Jul 18, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi list, does anyone have an example (input pdb, gmx commands and md.mdp for example) to test gromacs with and without openmm? The case I use here (with explicit water) didn't show me any speed up (comparing with mpirun -c 2 mdrun_mpi...). I am using Mac Leopard 10.5.7 with Cuda drivers and gromacs 4.0.5 This would be expected if you read the OpenMM README or see http://oldwiki.gromacs.org/index.php/OpenMM_GROMACS Mark -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ 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] query about topolgen.pl
subarna thakur wrote: Hi Can any body please tell me how to install and execute topolgen.pl script in linux for generationf topology file. It is not given in the Readme file. perl topolgen -h -Justin Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] query about topolgen.pl
Justin A. Lemkul wrote: subarna thakur wrote: Hi Can any body please tell me how to install and execute topolgen.pl script in linux for generationf topology file. It is not given in the Readme file. perl topolgen -h Sorry, that's the current in-house version. To execute: perl topolgen.pl (your .pdb file) -Justin Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] query regarding .top file
subarna thakur wrote: Hello I have generated .top file for an ligand with the mktop programm for OPLSAA force field , how do I include this .top file for the ligand along with that my protein in the gromacs run? You don't #include .top files, you #include .itp files. See the manual (Chapter 5) for relevant differences. -Justin Subarna Looking for local information? Find it on Yahoo! Local http://in.rd.yahoo.com/tagline_local_1/*http://in.local.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] parameters for Phosphorylated threonine and serine
Hi, Can anyone suggest me where to get phosphorylated ser and threonine parameters ? Regards, Nikhil Looking for local information? Find it on Yahoo! Local http://in.local.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
Re: [gmx-users] parameters for Phosphorylated threonine and serine
nikhil damle wrote: Hi, Can anyone suggest me where to get phosphorylated ser and threonine parameters ? The ffG43a1p tarball is available under User Contributions on the Gromacs website: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields As I recall, there were some formatting problems with some of the files (they were made under a very old Gromacs version, and some formatting has since changed). If you run into problems, you may contact me off-list; I should have the corrected files. -Justin Regards, Nikhil Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] CPU Usage
Hello Dear GMX Users, I have installed Gromacs 4 on a Quad PC. However, when I RUN the example (Water), the CPU usage is just 25%. It means that just one of the four CPUs are used. Please help me how I can change the status of calculation for using all of the four CPUs. Thank you very much in advance. Mahmoud ___ 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] x2top hangs
Folks -- I cannot manage to get x2top to work on even the simplest example. Here is ethane.pdb, a PDB file for ethane (built using Avogadro, with the CONECT records stripped out): COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.2.2b1 ATOM 1 C LIG 1 -3.466 -1.641 -0.001 1.00 0.00 C ATOM 2 C LIG 1 -1.954 -1.689 0.025 1.00 0.00 C ATOM 3 H LIG 1 -3.817 -0.605 0.026 1.00 0.00 H ATOM 4 H LIG 1 -3.882 -2.168 0.863 1.00 0.00 H ATOM 5 H LIG 1 -3.850 -2.112 -0.910 1.00 0.00 H ATOM 6 H LIG 1 -1.570 -1.218 0.934 1.00 0.00 H ATOM 7 H LIG 1 -1.538 -1.163 -0.839 1.00 0.00 H ATOM 8 H LIG 1 -1.603 -2.726 -0.002 1.00 0.00 H END I try to run the following command under GROMACS 4.0, x2top -f ethane.pdb -o ethane.top with the most recent version of the file ffoplsaa.n2t in its proper place (/usr/local/gromacs/share/gromacs/top/), and I get the following output: ... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 0 ... and then the program hangs. Can someone confirm that x2top actually works, and send a simple working example to me? Scott Milner William H. Joyce Professor The Pennsylvania State University Department of Chemical Engineering 120 Fenske Laboratory University Park, PA 16802 (814) 863-9355 smil...@engr.psu.edu ___ 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] CPU Usage
mahmoud mirzaei wrote: Hello Dear GMX Users, I have installed Gromacs 4 on a Quad PC. However, when I RUN the example (Water), the CPU usage is just 25%. It means that just one of the four CPUs are used. Please help me how I can change the status of calculation for using all of the four CPUs. You need to install an MPI implementation, and configure Gromacs with --enable-mpi. -Justin Thank you very much in advance. Mahmoud ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] x2top hangs
Scott Milner wrote: Folks -- I cannot manage to get x2top to work on even the simplest example. Here is ethane.pdb, a PDB file for ethane (built using Avogadro, with the CONECT records stripped out): COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.2.2b1 ATOM 1 C LIG 1 -3.466 -1.641 -0.001 1.00 0.00 C ATOM 2 C LIG 1 -1.954 -1.689 0.025 1.00 0.00 C ATOM 3 H LIG 1 -3.817 -0.605 0.026 1.00 0.00 H ATOM 4 H LIG 1 -3.882 -2.168 0.863 1.00 0.00 H ATOM 5 H LIG 1 -3.850 -2.112 -0.910 1.00 0.00 H ATOM 6 H LIG 1 -1.570 -1.218 0.934 1.00 0.00 H ATOM 7 H LIG 1 -1.538 -1.163 -0.839 1.00 0.00 H ATOM 8 H LIG 1 -1.603 -2.726 -0.002 1.00 0.00 H END I try to run the following command under GROMACS 4.0, x2top -f ethane.pdb -o ethane.top with the most recent version of the file ffoplsaa.n2t in its proper place (/usr/local/gromacs/share/gromacs/top/), and I get the following output: ... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 0 ... and then the program hangs. Can someone confirm that x2top actually works, and send a simple working example to me? The 4.0.x versions of x2top do not work, as far as I know. The code is undergoing major changes. Version 3.3.3 should be operable, if memory serves. -Justin Scott Milner William H. Joyce Professor The Pennsylvania State University Department of Chemical Engineering 120 Fenske Laboratory University Park, PA 16802 (814) 863-9355 smil...@engr.psu.edu ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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: openmm
Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp? ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented My full md.mdp file is: integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 comm_mode = ANGULAR Many thanks in advance, Alan On Sat, Jul 18, 2009 at 11:35, Alanalanwil...@gmail.com wrote: Dear Mark, Thanks. I reread those file carefully and noticed the only implicit solvent. Sorry for that. I am building my test case here to see by myself how fast it can be. Alan On Sat, Jul 18, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi list, does anyone have an example (input pdb, gmx commands and md.mdp for example) to test gromacs with and without openmm? The case I use here (with explicit water) didn't show me any speed up (comparing with mpirun -c 2 mdrun_mpi...). I am using Mac Leopard 10.5.7 with Cuda drivers and gromacs 4.0.5 This would be expected if you read the OpenMM README or see http://oldwiki.gromacs.org/index.php/OpenMM_GROMACS Mark -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ 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: openmm
Alan wrote: Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp? ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented snip rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 You need to set rlist = rcoulomb = rvdw, otherwise, by definition, you have a twin-range setup. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] mdp file for monitoring pair groups
The problem is that the .tpr file tells me that the monitoring is being made between all pairs. I want only the pairs aminoacid1-ligand, aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of monitoring, i.e., between all possible pairs, gives me .edr files that are 1Gb or more in size. That is a problem since I need to do the same type of analysis for 61 more complexes. So, again, I need to monitor only the pairs in which one of the members is the LIGAND and the other is one of the aminoacids of that huge list I posted in the energygrps. what is not working exactly? This should give you as output all the pair interacts and you can select the ones you want ... ?! On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote: I have created an mdp file with 202 groups for monitoring in the energygrps string. Being 201 of these aminoacids which interact with the 202nd which is the ligand. The problem is that I found out that this does not work properly, and also does not work the way I thought it would work. Well, the deal is that I want to monitor each of the pair interactions, i.e., aminoacid1-ligand, aminoacid2-ligand, aminoacid3-ligand etc. Is there a way I can do this with a single mdp file, or should I create 202 different mdp files and -rerun 202 times the same simulation (which sounds just as crazy as the idea i had before)? Here is what I have written for the energygrps: energygrps = _S r_29 r_30 r_61 r_63 r_64 r_65 r_66 r_67 r_68 r_69 r_70 r_71 r_72 r_73 r_74 r_75 r_76 r_77 r_78 r_79 r_80 r_81 r_82 r_83 r_84 r_85 r_86 r_87 r_88 r_92 r_94 r_95 r_96 r_98 r_111 r_112 r_113 r_114 r_115 r_116 r_117 r_118 r_119 r_120 r_121 r_122 r_123 r_124 r_125 r_126 r_127 r_128 r_129 r_130 r_131 r_132 r_133 r_134 r_142 r_143 r_144 r_145 r_146 r_147 r_148 r_149 r_150 r_151 r_152 r_154 r_172 r_195 r_196 r_197 r_198 r_199 r_200 r_201 r_202 r_203 r_222 r_223 r_224 r_225 r_226 r_227 r_228 r_231 r_232 r_233 r_234 r_243 r_246 r_247 r_249 r_250 r_251 r_275 r_277 r_278 r_279 r_280 r_281 r_282 r_283 r_284 r_285 r_286 r_287 r_288 r_289 r_290 r_291 r_292 r_293 r_294 r_295 r_296 r_297 r_325 r_326 r_327 r_328 r_329 r_330 r_331 r_332 r_333 r_334 r_335 r_336 r_337 r_338 r_339 r_340 r_341 r_342 r_343 r_344 r_345 r_346 r_354 r_355 r_356 r_357 r_358 r_359 r_360 r_361 r_362 r_363 r_364 r_365 r_367 r_368 r_369 r_370 r_371 r_378 r_395 r_396 r_397 r_398 r_399 r_401 r_402 r_403 r_424 r_426 r_430 r_432 r_433 r_434 r_435 r_438 r_439 r_440 r_441 r_442 r_443 r_444 r_445 r_446 r_447 r_448 r_449 r_450 r_451 r_452 r_453 r_456 r_458 r_459 r_460 r_461 r_476 r_521 r_536 r_537 r_538 r_539 I would like some advice on the matter. Thank you in advance Fabrício Bracht ___ 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] mdp file for monitoring pair groups
Ragnarok sdf wrote: The problem is that the .tpr file tells me that the monitoring is being made between all pairs. I want only the pairs aminoacid1-ligand, aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of monitoring, i.e., between all possible pairs, gives me .edr files that are 1Gb or more in size. That is a problem since I need to do the same type of analysis for 61 more complexes. So, again, I need to monitor only the pairs in which one of the members is the LIGAND and the other is one of the aminoacids of that huge list I posted in the energygrps. Gromacs is working as it should. I don't believe there is any way to specify an energy pair as you want it. To consider 200+ interactions, you have the side effect of getting a 200x200 matrix of interactions. Does your ligand really interact with 200 amino acids, or does it potentially interact with 200 amino acids? If you run the trajectory to see which amino acids are actually interacting, you can -rerun with substantially less energy groups defined. -Justin what is not working exactly? This should give you as output all the pair interacts and you can select the ones you want ... ?! On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote: I have created an mdp file with 202 groups for monitoring in the energygrps string. Being 201 of these aminoacids which interact with the 202nd which is the ligand. The problem is that I found out that this does not work properly, and also does not work the way I thought it would work. Well, the deal is that I want to monitor each of the pair interactions, i.e., aminoacid1-ligand, aminoacid2-ligand, aminoacid3-ligand etc. Is there a way I can do this with a single mdp file, or should I create 202 different mdp files and -rerun 202 times the same simulation (which sounds just as crazy as the idea i had before)? Here is what I have written for the energygrps: energygrps = _S r_29 r_30 r_61 r_63 r_64 r_65 r_66 r_67 r_68 r_69 r_70 r_71 r_72 r_73 r_74 r_75 r_76 r_77 r_78 r_79 r_80 r_81 r_82 r_83 r_84 r_85 r_86 r_87 r_88 r_92 r_94 r_95 r_96 r_98 r_111 r_112 r_113 r_114 r_115 r_116 r_117 r_118 r_119 r_120 r_121 r_122 r_123 r_124 r_125 r_126 r_127 r_128 r_129 r_130 r_131 r_132 r_133 r_134 r_142 r_143 r_144 r_145 r_146 r_147 r_148 r_149 r_150 r_151 r_152 r_154 r_172 r_195 r_196 r_197 r_198 r_199 r_200 r_201 r_202 r_203 r_222 r_223 r_224 r_225 r_226 r_227 r_228 r_231 r_232 r_233 r_234 r_243 r_246 r_247 r_249 r_250 r_251 r_275 r_277 r_278 r_279 r_280 r_281 r_282 r_283 r_284 r_285 r_286 r_287 r_288 r_289 r_290 r_291 r_292 r_293 r_294 r_295 r_296 r_297 r_325 r_326 r_327 r_328 r_329 r_330 r_331 r_332 r_333 r_334 r_335 r_336 r_337 r_338 r_339 r_340 r_341 r_342 r_343 r_344 r_345 r_346 r_354 r_355 r_356 r_357 r_358 r_359 r_360 r_361 r_362 r_363 r_364 r_365 r_367 r_368 r_369 r_370 r_371 r_378 r_395 r_396 r_397 r_398 r_399 r_401 r_402 r_403 r_424 r_426 r_430 r_432 r_433 r_434 r_435 r_438 r_439 r_440 r_441 r_442 r_443 r_444 r_445 r_446 r_447 r_448 r_449 r_450 r_451 r_452 r_453 r_456 r_458 r_459 r_460 r_461 r_476 r_521 r_536 r_537 r_538 r_539 I would like some advice on the matter. Thank you in advance Fabrício Bracht ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] Conversion
Dear gromacs users, How can I convert a certain concentration of a compound (say in mg/ml) to be used in my simulations, into number of molecules to be added in the system??? Please help. See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.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] Re: openmm
Thanks Justin. I could swear I tried what you said... anyway it worked now (2.5 x faster), but not with implicit solvent for mdrun-openmm... Trying with plain mdrun with the setup for implicit solvent and it seemed to work (although I don't know how to interpret this from GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: even though this is not available in the standard Gromacs 4) I still would like an example/tutorial that really worked for someone with gmx openmm. In the end, with mdrun-openmm and implicit solvent in the mdp file, I got a file md.gro full of nan nan. For those interested, here are the commands I did. If you have GMX with ffamber, CUDA and GMX-openmm you may reproduce it. ### cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = Reaction-Field ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step epsilon_rf = 0 pbc = no EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no comm_mode = ANGULAR ; uncomment below to test with implicit solvent ;implicit_solvent = GBSA ;gb_algorithm = OBC ;gb_epsilon_solvent = 78.3 EOF wget -c http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdbcompression=NOstructureId=1BVG; -O 1BVG.pdb grep 'ATOM ' 1BVG.pdb| Protein.pdb grep 'HETATM' 1BVG.pdb| Ligand.pdb sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \ | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \ | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \ | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g | ProteinAmber.pdb # Process with pdb2gmx and define water pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -ignh grompp -f em.mdp -c Protein2.pdb -p Protein.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr # OK mdrun-openmm -v -deffnm md # 3 times fater # works fine without set for implicit solvent in md.mdp # with implicit solvent, md.gro full of nan nan nan everywhere. ### On Sat, Jul 18, 2009 at 17:31, Alanalanwil...@gmail.com wrote: Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp? ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented My full md.mdp file is: integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist = 1.0 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 comm_mode = ANGULAR Many thanks in advance, Alan On Sat, Jul 18, 2009 at 11:35, Alanalanwil...@gmail.com wrote: Dear Mark, Thanks. I reread those file carefully and noticed the only implicit solvent. Sorry for that. I am building my test case here to see by myself how fast it can be. Alan On Sat, Jul 18, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi list, does anyone have an example (input pdb, gmx commands and md.mdp for example) to test gromacs with and without openmm? The case I use here (with explicit water) didn't show me any speed up (comparing with mpirun -c 2 mdrun_mpi...). I am using Mac Leopard 10.5.7 with Cuda drivers and gromacs 4.0.5 This
Re: [gmx-users] Conversion
P.R.Anand Narayanan wrote: Dear gromacs users, How can I convert a certain concentration of a compound (say in mg/ml) to be used in my simulations, into number of molecules to be added in the system??? Basic general chemistry: from mg/mL to molarity, then to number of molecules per unit volume. -Justin Please help. See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] DNA SIMULATION
Dear gmxuser Does somebody knows how to simulate the DNA in gromacs?? I know it is so general question but I need some hint. 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] DNA SIMULATION
Morteza Khabiri wrote: Dear gmxuser Does somebody knows how to simulate the DNA in gromacs?? I know it is so general question but I need some hint. Check out the amber force field with gromacs web site. 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 -- 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://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: openmm
Alan wrote: Thanks Justin. I could swear I tried what you said... anyway it worked now (2.5 x faster), but not with implicit solvent for mdrun-openmm... Trying with plain mdrun with the setup for implicit solvent and it seemed to work (although I don't know how to interpret this from GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: even though this is not available in the standard Gromacs 4) From the link I supplied yesterday: 'Neither cutoffs nor periodic boundary conditions are supported. The coulombtype and vdwtype settings are ignored, as are the various cutoff settings.' So if this still pertains to your version, your attempt to use reaction-field was not useful. I still would like an example/tutorial that really worked for someone with gmx openmm. You will need to contact the people who wrote it. I am not aware that any of them post here. In the end, with mdrun-openmm and implicit solvent in the mdp file, I got a file md.gro full of nan nan. All I know is what I can read in the README. 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] Changing gmx_msd.c
Jennifer Williams wrote: Hi gmx_users, I am trying to use NEMD to get transport diffusion coefficients. I am adding an acceleration to my atoms in the z direction and then I need to calculate this quantity: 1/t ? [r(t) ? r(0)] My plan was to alter the code that calculates the MSD (gmx_msd.c located in src/tools). This calculates; 1/t 1/N. ? [r(t) ? r(0)]^2 I presumed that all I needed to do was locate and remove the squared function and the division by the number of molecules (1/N). I would also change the factor for the conversion of nm^2/ps to 10e-5 cm^2/s since I would now be doing nm/ps to 10e-5 cm/s. I'll have to guess you're correct, since I can't read the symbols you're intending. However my problem is that I have never worked with C++ so changing the code involved some guess-work. GROMACS is written in C, not C++, by the way :-) For the removal of the square I did; r2 += rv[m]*rv[m];r2 += rv[m]; (line 252) r2 += r*r; r2 += r;(line 270) to remove the division by the number of molecules (1/N), I removed line g/=nx; (line 279) I realise that these changes are only valid for the first case CASE (static_real_calc_norm), which I presumed was for the basic calculation invoked by this command; Assumption is a short route to madness when programming. You should look at the code from which the relevant function is called and see what preconditions are required for it. Stepping through the code with a debugger is probably a good way to understand the flow. g_msd ?f traj.xtc ?s md.tpr i.e. I don?t plan on using ?pbc ?mol etc so I didn?t change the code for these cases. (I also realise that unless I change the code, the calculated error wont be valid-but I was going to worry about that later!) However, the changes I made do not change the output from that of the original MSD code. I am using the correct, changed executable and not an old one (i.e I copied the compiled executable to gromacs/bin). So it looks like I am not changing the correct part of the code, or perhaps the command line g_msd ?f traj.xtc ?s md.tpr is not changing the case I altered? You can just run $builddir/src/tools/g_msd rather than installing a potentially problematic version. Adding a printf statement which is unique to your version will help you feel confident you're using the right version. Has anyone else changed the code for this purpose or would anyone be able to give me some pointers on what I need to alter in the code. Today is the first time I have ever looked at any C++ code (though I know some fortran) so please be as specific as possible :) There are easier things in life than modifying code written by someone else in an unfamiliar programming language (e.g. juggling knives while dictating a symphony) but you seem to be in the ballpark. 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] Peptide - DMPC membrane simulations - Unstable system
Hello gain Justin, Now I figured out that the problem was in gromacs version 4.0. So peptide in water works no problem. I have used trjconv -pbc mol -ur compact and it solved the artifact problem. Thanks a lot! Now I have started simulation on 96 CPU's for 1000ns total run time. But after 1 day simulation the system crashed or exploded with the following error: [First time it failed because of some problems with the server, and then I have resumed the run using tpbconv -s DMPCRun1000ns.tpr -f 1000nsDMPCA141Run_part1.trr -extend 10 -o DMPCRun100nspart2.tpr] vol 0.78 imb F 2% pme/F 2.15 step 10578400, will finish Sat Aug 29 07:23:01 2009 vol 0.77 imb F 3% pme/F 2.15 step 10578500, will finish Sat Aug 29 07:28:32 2009 Step 10578599, time 21157.2 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.299801, max 6.073617 (between atoms 9449 and 9450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9451 9468 93.60.1530 0.1293 0.1530 Fatal error: 15 particles communicated to PME node 6 are more than a cell length out of the domain decomposition cell of their charge group I am attaching my mdp files used to to EM and MDrun here: EM: http://kbessonov.googlepages.com/em_lipid.mdp MD: http://kbessonov.googlepages.com/mdonly_1000ns.mdp I was wondering why my system fails. and what can I do to avoid it? I was thinking maybe to run several times EM on the system, maybe it will help? What bugs me is that it fails really late in simulation. I have not seen trajectory file yet. ___ 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] Insert a certain number of water molecules into a nanotube
nbsp;Dear all: nbsp; nbsp;nbsp;nbsp;nbsp; I am trying to insert a certain number of water molecules into a nanotube with Gromacs-4.0.5. When I input the command genbox -cp tube.gro -ci spc216.gro -nmol 328 -try 20 -o, I get the following error. nbsp; Program genbox, VERSION 4.0.5 Source code file: gmx_genbox.c, line: 318 nbsp; Fatal error: more then one residue in insert molecules program terminated nbsp; Should the insert molecules be no more than one residue? If it should be, how can I insert 328 water molecules into the tube? Are there any other commands in Gromacs that can be used for the same thing? nbsp; Thank you in advance! ___ 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
