Re: [gmx-users] parallel simulation in dual core PC
Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro -np 2 -- at least this is what I understand from what my prof told me. We just started running parallel simulations for an undergraduate research project and I believe that is how we input commands. I'm sure the gromacs experts will correct me if I'm wrong. Good luck! Arden On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin wrote: > Hi, > > I want to use my dual core PC to do the simulation. > The version of GROMACS installed is version 4.0.5. > According the message post by others on mailing list before. > I type "lamboot" first, and type the commend: > mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log > -c 200ns.gro. > When the simulation starts, I use the commend, "top", to check the utility > of CPU. > I found there is only one core which is used by GROMACS. > And the utility of this core is separated to 52% and 48% for two mdrun_mpi > jobs. > How can I do for that? > Any and all assistance is greatly appreciated. > > Hsin-Lin > > -- > 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
[gmx-users] Literature for DNA Binding Protein Simulations
Dear GROMACS users, I am interested in running a simulation of a DNA-binding peptide and a short stretch of DNA for an undergraduate research project. The pdb file we will be using is a modified version of the Hickman et. al (2004) Rep structure http://www.pdb.org/pdb/explore/explore.do?structureId=1RZ9 . The file consists of five Rep peptides and one stretch of DNA (approx. 6 helical turns). We will only be simulating one peptide however, at 197 aa. We would like to subject the peptide to different variables in a water-solvated box and then observe its interaction with the segment of DNA to which it binds (such as temperature, ion molarities, etc). What literature would you recommend I review in order to have a good understanding of the parameters involved in such a simulation? I have run simulations of this peptide in solvated systems before, but I have never attempted one with more than one peptide or a peptide with DNA. Any suggestions would be very appreciated. Arden Perkins -- 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] Literature for DNA Binding Protein Simulations
Dear GROMACS users, I am interested in running a simulation of a DNA-binding peptide and a short stretch of DNA for an undergraduate research project. The pdb file we will be using is a modified version of the Hickman et. al (2004) Rep structure http://www.pdb.org/pdb/explore/explore.do?structureId=1RZ9 . The file consists of five Rep peptides and one stretch of DNA (approx. 6 helical turns). We will only be simulating one peptide however, at 197 aa. We would like to subject the peptide to different variables in a water-solvated box and then observe its interaction with the segment of DNA to which it binds (such as temperature, ion molarities, etc). What literature would you recommend I review in order to have a good understanding of the parameters involved in such a simulation? I have run simulations of this peptide in solvated systems before, but I have never attempted one with more than one peptide or a peptide with DNA. Any suggestions would be very appreciated. Arden Perkins -- 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] distance from solute atom to the edge of the box
Oh. You are correct. I've gotten a little rusty. Thanks! On Tue, Jan 12, 2010 at 9:10 AM, Justin A. Lemkul wrote: > > > Arden Perkins wrote: > >> Also, you can type " -h " in your terminal and it will bring up a list >> of commands and options for the program and can usually explain what they >> mean/do. For example: -h pdb2gmx >> > > Such a command is incorrect. The -h flag must follow the Gromacs tool, > otherwise you will undoubtedly receive "-h: command not found." > > -Justin > > Arden Perkins >> >> On Tue, Jan 12, 2010 at 4:17 AM, leila karami >> > karami.lei...@gmail.com>> wrote: >> >>Hi >>How is determined distance from solute atom to the edge of the box >>in editconf command (what criterion)? >> >>Any help will highly appreciated! >> >> >>-- >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before >>posting! >>Please don't post (un)subscribe requests to the list. Use the >>www interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 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] distance from solute atom to the edge of the box
Also, you can type " -h " in your terminal and it will bring up a list of commands and options for the program and can usually explain what they mean/do. For example: -h pdb2gmx Arden Perkins On Tue, Jan 12, 2010 at 4:17 AM, leila karami wrote: > Hi > > How is determined distance from solute atom to the edge of the box in > editconf command (what criterion)? > > > Any help will highly appreciated! > > -- > 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] SiO2 simulation
I believe pdb files (protein data bank) are only for peptides, so unless you are simulating a peptide you will not need any pdb files for your SiO2. Your structure file (.gro) for SiO2 may be in the fftw library files (or whatever forcefield you're using). Hope that helps. Arden Perkins On Tue, Jan 12, 2010 at 3:23 AM, Batistakis, C. wrote: > Dear all > > > > I am a new user of Gromacs. I am interested to simulate amorphous SiO2 and > I would like to know if someone can send me the .pdb and .top files. > > > > Thanks in advance > > > > Chrysostomos > > -- > 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] Why density increase with increasing the cutoff length?
>From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. Arden Perkins On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song wrote: > Dear Users: > > Anyone can explain why the density of the water models increase with > increase the cutoff length. I tried a couple water models in reaction-field, > PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the > same trend. Then there must be some reasons. Anyone can tell me why? > > -- > Yanmei Song > Ph.D. Candidate > Department of Chemical Engineering > Arizona State University > > -- > 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
[gmx-users] Charge neutralization
Hey all, I am trying to examine couplings between Mg+2 ions and a peptide with a -5 charge. I would like to optimize couplings and have considered using a +1 charge from the system. I read that GROMACS can do this and that in theory it should have the same effect as adding ions but it is not standard practice. For future simulations I plan to increase the [Mg+2] and am worried about couplings from Cl- if I were to use Cl- to neutralize the excess positive charge. Is it ok to use the system to neutralize these charges? Or is that considered a bad experimental design? Thanks for you feedback! Arden Perkins -- 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] Adding ions
I am an undergraduate student and I am still learning to use GROMACS. When I add my ions to the solution (using genion) by the procedure described in the funnel web spider tutorial the .gro and .top files do not match. I tried subtracting solvent molecules but they still dont match and I can't continue. What am I doing wrong? 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
