[gmx-users] About Zinc coordination
Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singam Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! 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
[gmx-users] About Zinc coordination
Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singa Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! 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
[gmx-users] (no subject)
Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singam Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! 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
RE: [gmx-users] About Zinc coordination
If you are new to Gromcs you must study all the documentation/tutorials/HowTo's first, in particular this one about parametrization of new molecules: http://www.gromacs.org/Documentation/How-tos/Parameterization Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of babu gokul Sent: 19 February 2010 08:12 To: gmx-users@gromacs.org Subject: [gmx-users] About Zinc coordination Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singa The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. -- 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] Assembling a good simulation starting point
Hello John, How large was the force after EM? Large forces often results in systems that explode during the simulation. Also, did you minimise with or without solvent? You assessment seems correct - the initial structure wasn't minimised and the tools of the trade are trying different conformations, minimising in vacuo at first and using other modelling tools before Gromacs. Also, read a bit in the mailing list and search the literature for similar studies. Good luck, Ran On Thu, 18 Feb 2010 19:08:11 -0800 (PST) John Ladasky blind.watchma...@yahoo.com wrote: Hello everyone, I'm a fairly new GROMACS user. I'm running GROMACS 4.0.5 on top of Ubuntu Linux 9.10. I am still learning a lot. I just tried to set up my first fairly complex simulation, and it failed. I have a protein of interest, a beta barrel with a hydrophobic, ligand-binding interior. I am interested in making mutations to this protein, with the goal of getting it to bind to a rather different ligand than the one it normally binds. The way that I propose to go about studying this problem is to construct a partially-unfolded version of the protein structure, add my ligand of interest, and then run an energy minimization. My first naive attempt to construct the partially-unfolded protein was not successful. I knew that it might have problems, but I tried it anyway. Using Biopython, I rotated the atomic coordinates so that the beta barrel was parallel to an axis. Then I simply pulled all of the atoms 3 Angstroms away from the axis. Finally, I inserted my ligand. Visually, inspecting the starting structure with PyMol, I didn't see anything egregious. However, I could have some unwanted close contacts. I got a few long bond warnings from pdb2gmx, but I persisted. I got through genbox, editconf, and my first grompp sucessfully. But then when I tried the first, position-restrained energy minimization, it aborted with too many LINCS warnings. I blew the system up. These LINCS warnings could come from close contacts, or from large forces in over-stretched bonds which resulted from my crude approach to expanding the protein structure. Whatever the cause, I need a smarter way to start. I am open to ANY suggestions! What I THINK I might want to do is to manipulate the starting structure in a more natural way. For example, selecting some peptide bonds in the beta turns, and changing their angles. A program which allows me to manipulate structures, and not just simulate natural forces, is what I think I need. Surely, people who have used GROMACS will have faced problems simliar to mine. Thanks for your advice! John Ladasky -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Skype: ran.friedman -- -- 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:Indexing specific atoms
Hello, Can anyone tell, how to index two specific atoms, (one form protein and one from ligand) eg; 440th atom of protein 450th atom of small molecule or OED of small molecule. My second question is: how to calculate the distance b/w these two atoms. i tried g_dist by including the indexed file with this, but the graph displays a wrong answer. thanks In advance. Parthiban. -- 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:Indexing specific atoms
Hello Parthiban, Can you elaborate more on the 'wrong answer'? Perhaps the following link can shed some light on the 'wrong' answer: http://lists.gromacs.org/pipermail/gmx-users/2009-March/040276.html [Deals with g_dist and PBC] Regards, -Shay Quoting parthi...@ncbs.res.in: Hello, Can anyone tell, how to index two specific atoms, (one form protein and one from ligand) eg; 440th atom of protein 450th atom of small molecule or OED of small molecule. My second question is: how to calculate the distance b/w these two atoms. i tried g_dist by including the indexed file with this, but the graph displays a wrong answer. thanks In advance. Parthiban. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:Indexing specific atoms
shaya...@post.tau.ac.il skrev: Hello Parthiban, Can you elaborate more on the 'wrong answer'? Perhaps the following link can shed some light on the 'wrong' answer: http://lists.gromacs.org/pipermail/gmx-users/2009-March/040276.html [Deals with g_dist and PBC] Regards, -Shay Quoting parthi...@ncbs.res.in: Hello, Can anyone tell, how to index two specific atoms, (one form protein and one from ligand) eg; 440th atom of protein 450th atom of small molecule or OED of small molecule. The format of the index files is simple. You can easily write a script to accomplish waht you want, or even do it manually. First you need to add the name of the index group, [ the_name ] Then follows the list of atoms belonging to the group. If you want the 440h atom of the protein, then just write 440 plus the number of the first atom in the protein. So if your protein starts at atom no 123, then its 440 atom will be number 563. Your index group will look something like this: [ the_440th_protein_atom ] 563 This you can do with the text editor of your choice. Simple as that. Erik My second question is: how to calculate the distance b/w these two atoms. i tried g_dist by including the indexed file with this, but the graph displays a wrong answer. thanks In advance. Parthiban. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Hi E R Azhagiya singam, You first have to ask yourself whether you're up to it. This is considered an advanded topic. In particular for groups like these. To start with, do you know the protonation state of the Zn(Cys)4 group in your case? Cheers, Tsjerk On Fri, Feb 19, 2010 at 9:14 AM, babu gokul bb...@yahoo.co.in wrote: Dear all I would like to simulate the molecule which consist of a zn atom coordinated to four CYS residue. I would like to know how to insert the parameters for zn coordination. As I am new to Gromacs I would like to have detailed description.I would like to use OPLS force field. Thanking you E R Azhagiya singam -- The INTERNET now has a personality. YOURS! See your Yahoo! Homepagehttp://in.rd.yahoo.com/tagline_yyi_1/*http://in.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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] Help with Segmentation fault!!!
But what is the real problem about the use of -DFLEXIBLE? Will I get wrong calculations from MD if I define it? Or it is just a matter of time (DFLEXIBLE = take longer) ?? 2010/2/18 Tsjerk Wassenaar tsje...@gmail.com Hi Deisy, define = -DFLEXIBLE integrator = md Well, probably you'd be better off with 'integrator = steep'. If you're doing MD, better not define -DFLEXIBLE. But for the rest, you give little account of what you're doing. What about the workflow, where in your scheme are we? What are you trying to do? How about some tutorial material? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- 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] Help with Segmentation fault!!!
- Original Message - From: Maurício Menegatti Rigo mauriciomr1...@gmail.com Date: Friday, February 19, 2010 22:28 Subject: Re: [gmx-users] Help with Segmentation fault!!! To: Discussion list for GROMACS users gmx-users@gromacs.org But what is the real problem about the use of -DFLEXIBLE? Will I get wrong calculations from MD if I define it? Or it is just a matter of time (DFLEXIBLE = take longer) ?? Justin's answer explained why. Did you see it? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Coefficients for user-defined tabulated potentials (topol.top + table.xvg)
Hello ! I would like to have some information about how to set the coefficients for tabulated potentials. I'm using coulombtype ewald and vdwtype user so I have to define tables for each pair of atoms (and/or one table all the rest of them) : table.xvg table_Si_O.xvg table_Si_Si.xvg table_O_O.xvg I've created these tables but I dont understand how to set the C6 and C12 coefficients : in the topology, the directive [ nonbond_params ] can be used to define C6 and C12 coefficients but only for lennard jones and buckingham potentials (I did'nt find how to set it for user tables in the manual nor in the mailing list). I've managed to run simulations by including C6 and C12 directly in the tables and define atomtypes with C6 and C12 set to 1.0 so that applying combination rule gives C6=1.0 and C12=1.0 for all pair of atoms but it would be much more convenient if the coefficients were set explicitly in the topology and not in the user tables. Thanks in advance -- --- David Waroquiers, Phd Student European Theoretical Spectroscopy Facility (ETSF) Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain (UCL) --- Address : Bâtiment Boltzmann Place Croix du Sud, 1 1348 Louvain-la-Neuve, Belgique --- E-mail : david.waroqui...@uclouvain.be Tel : + 32 (0)10 / 47 28 38 Fax : + 32 (0)10 / 47 34 52 --- -- 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] Backbone and MainChain
Hi From Gromacs Manual: - Backbone: all protein backbone atoms (C-alpha, N, C) - MainChain: backbone atoms, plus the carbonyl oxygens The following is part of .gro file. I listed the atom number, are those all correct ? C-alpha: 161,170,179 N:158,163, 172 C: ??? what does this C represent ? carbonyl oxygens: 162,171,180 Thank you Lin 16GLY N 158 4.365 -0.145 3.067 -0.6971 -0.0210 0.0556 16GLY H 159 4.280 -0.127 3.017 0.4468 0.2941 -1.8808 16GLY CA 160 4.377 -0.037 3.166 -0.3605 0.4870 -0.5237 16GLY C 161 4.250 -0.037 3.252 0.0432 -0.0265 0.0901 16GLY O 162 4.180 -0.137 3.266 0.2570 -0.1341 0.3963 17LEU N 163 4.216 0.087 3.287 0.7572 0.0242 0.6305 17LEU H 164 4.276 0.160 3.254 0.7410 -0.8313 -1.4811 17LEU CA 165 4.102 0.123 3.372 -0.0401 -0.2644 -0.2910 17LEU CB 166 4.156 0.220 3.477 0.1016 -0.1889 -0.4337 17LEU CG 167 4.275 0.181 3.566 -0.0012 -0.5604 -0.4598 17LEUCD1 168 4.338 0.303 3.632 1.2085 -0.9864 -0.7919 17LEUCD2 169 4.233 0.084 3.676 0.8349 -0.3795 0.0241 17LEU C 170 3.980 0.184 3.303 -0.0634 0.2558 0.2056 17LEU O 171 3.993 0.297 3.258 -0.2180 0.0717 -0.3035 18ASP N 172 3.867 0.113 3.302 0.0759 0.0338 -0.0172 18ASP H 173 3.855 0.036 3.364 -0.9960 1.0931 1.1466 18ASP CA 174 3.744 0.153 3.233 -0.1100 -0.0437 0.2680 18ASP CB 175 3.638 0.047 3.201 -0.1316 0.1250 -0.2304 18ASP CG 176 3.612 -0.052 3.315 -0.1959 0.1668 -0.2089 18ASPOD1 177 3.588 -0.170 3.282 0.1094 0.1194 -0.2643 18ASPOD2 178 3.643 -0.033 3.435 -0.2608 -0.1375 -0.1441 18ASP C 179 3.665 0.270 3.294 0.1485 0.2274 0.0883 18ASP O 180 3.660 0.382 3.245 -0.2873 0.2105 0.0864 -- 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] domain decomposition and load balancing
Hi Everyone, I am trying to run a simulation with the option pbc=xy turned on. I am using 64 processors for the simulation. The mdrun_mpi evokes the following error message before starting the md steps There is no domain decomposition for 64 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition This has to do with the load balancing in the domain decomposition version of mdrun. Can anyone suggest me how to set the option -rdd or -dds? Also the simulation runs fine on one node (with domain decomposition) and with particle decomposition but both of them extremely slow. Thank you, Amit -- 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] domain decomposition and load balancing
- Original Message - From: Amit Choubey kgp.a...@gmail.com Date: Saturday, February 20, 2010 8:51 Subject: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Everyone, I am trying to run a simulation with the option pbc=xy turned on. I am using 64 processors for the simulation. The mdrun_mpi evokes the following error message before starting the md steps There is no domain decomposition for 64 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition This has to do with the load balancing in the domain decomposition version of mdrun. Can anyone suggest me how to set the option -rdd or -dds? Those options are not normally the problem - but see the log file for info and mdrun -h for instructions. You should read up in the manual about domain decomposition, and see about choosing npme such that 64-npme is a number that is suitably composite that you can make a reasonably compact 3D grid so that the minimum cell size is not a constraint. Cells have to be large enough that all nonbonded interactions can be resolved in consultation with at most nearest-neighbour cells (and some other constraints). I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45 gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the cells to have the smallest diameter possible. Of course if your simulation box is so small that the 2D DD for pbc=xy will always lead to slabs that are too small in one dimension then you can't solve this problem with DD. If pbc=xy permits a 3D DD, then the same considerations apply. npme=19 gives 5x3x3 but npme=28 allows 4x3x3 Also the simulation runs fine on one node (with domain decomposition) and with particle decomposition but both of them extremely slow. Well, that's normal... 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] domain decomposition and load balancing
Hi Mark, I am not using PME calculation. I was hoping mdrun will do the cell allocation itself. Thanks, Amit On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com Date: Saturday, February 20, 2010 8:51 Subject: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Everyone, I am trying to run a simulation with the option pbc=xy turned on. I am using 64 processors for the simulation. The mdrun_mpi evokes the following error message before starting the md steps There is no domain decomposition for 64 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition This has to do with the load balancing in the domain decomposition version of mdrun. Can anyone suggest me how to set the option -rdd or -dds? Those options are not normally the problem - but see the log file for info and mdrun -h for instructions. You should read up in the manual about domain decomposition, and see about choosing npme such that 64-npme is a number that is suitably composite that you can make a reasonably compact 3D grid so that the minimum cell size is not a constraint. Cells have to be large enough that all nonbonded interactions can be resolved in consultation with at most nearest-neighbour cells (and some other constraints). I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45 gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the cells to have the smallest diameter possible. Of course if your simulation box is so small that the 2D DD for pbc=xy will always lead to slabs that are too small in one dimension then you can't solve this problem with DD. If pbc=xy permits a 3D DD, then the same considerations apply. npme=19 gives 5x3x3 but npme=28 allows 4x3x3 Also the simulation runs fine on one node (with domain decomposition) and with particle decomposition but both of them extremely slow. Well, that's normal... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] domain decomposition and load balancing
Hi Mark, I dont think i need to play with npme at all. Amit On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey kgp.a...@gmail.com wrote: Hi Mark, I am not using PME calculation. I was hoping mdrun will do the cell allocation itself. Thanks, Amit On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Amit Choubey kgp.a...@gmail.com Date: Saturday, February 20, 2010 8:51 Subject: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Everyone, I am trying to run a simulation with the option pbc=xy turned on. I am using 64 processors for the simulation. The mdrun_mpi evokes the following error message before starting the md steps There is no domain decomposition for 64 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition This has to do with the load balancing in the domain decomposition version of mdrun. Can anyone suggest me how to set the option -rdd or -dds? Those options are not normally the problem - but see the log file for info and mdrun -h for instructions. You should read up in the manual about domain decomposition, and see about choosing npme such that 64-npme is a number that is suitably composite that you can make a reasonably compact 3D grid so that the minimum cell size is not a constraint. Cells have to be large enough that all nonbonded interactions can be resolved in consultation with at most nearest-neighbour cells (and some other constraints). I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45 gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the cells to have the smallest diameter possible. Of course if your simulation box is so small that the 2D DD for pbc=xy will always lead to slabs that are too small in one dimension then you can't solve this problem with DD. If pbc=xy permits a 3D DD, then the same considerations apply. npme=19 gives 5x3x3 but npme=28 allows 4x3x3 Also the simulation runs fine on one node (with domain decomposition) and with particle decomposition but both of them extremely slow. Well, that's normal... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] domain decomposition and load balancing
- Original Message - From: Amit Choubey kgp.a...@gmail.com Date: Saturday, February 20, 2010 10:25 Subject: Re: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Mark and Justin, I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie (60nm) side. I tried using only two nodes, it gives the same error There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition ... so what does the log file say? Mark On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Saturday, February 20, 2010 10:13 Subject: Re: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users gmx-users@gromacs.org Amit Choubey wrote: Hi Mark, I am not using PME calculation. I was hoping mdrun will do the cell allocation itself. It will, unless it can't, which is exactly your problem. Mark's point stands, regardless of whether or not you're using PME. DD requires certain minimum size requirements (which are discussed in the manual and the Gromacs 4 paper), so you have two choices: 1. Read about the options mdrun is telling you about. 2. Use fewer nodes so that the DD algorithm can construct reasonably-sized domains. 3. Use a larger simulation system so the minimum cell size is larger w.r.t. the cutoffs 4. (If reasonable) Don't use pbc=xy Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] domain decomposition and load balancing
the log file just lists all the parameters of the simulation, following is a
part of it
parameters of the run:
integrator = md
nsteps = 4000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode= Linear
nstlog = 1000
nstxout = 1000
nstvout = 0
nstfout = 500
nstenergy= 10
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xy
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.3
rtpi = 0.05
coulombtype = Reaction-Field-zero
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Shift
rvdw_switch = 0.9
rvdw = 1
epsilon_r= 1
epsilon_rf = inf
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 2
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 3.92594e+06
ref_t: 0
tau_t: 0
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 0 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
On Fri, Feb 19, 2010 at 3:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Saturday, February 20, 2010 10:25
Subject: Re: [gmx-users] domain decomposition and load balancing
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi Mark and Justin,
I am using a box of size
[gmx-users] Normal Mode analysis
Hello everyone, I am trying to do normal mode analysis for a protein using Gromacs. Can anyone point me out towards a sample mdp file that I could edit for this purpose? Thanks Ajit B. -- 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
