[gmx-users] Re: NAMD simulation in Gromacs
Oguz, in case you want to try the psfgen patch, it is now available for download on our group website at http://cmb.ornl.gov/resources/developments/top-patch-for-psfgen http://cmb.ornl.gov/resources/developments/top-patch-for-psfgenRoland On Thu, Sep 30, 2010 at 7:28 PM, Roland Schulz rol...@utk.edu wrote: Oguz, On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak gurbulako...@yahoo.comwrote: Dear Dr. Roland Schulz, Thank you very much for your attention. I would like to have a copy of patch that generates gromacs topology from psf file. And could you please explain how to use this patch in detail ? Because I have no information on Pär's scripts. Do you have standard CHARMM or Amber FF? Than you don't need to convert the FF because it is already part of GROMACS. I think, In order to continue a NAMD simulation in Gromacs I should first save the last coordinates (.coor file in namd ) as a pdb file and convert it into gro file . But there are many ways to get a gro file no you don't need to convert the coordinate file or get the last frame. - using pdb2gmx ( but I should choose the force field in gromacs. This may be a problem. ) By the way, I changed CHARMM force field and use Amber type force field in NAMD. Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a standard molecule (e.g. protein), it will be much easier to just use pdb2gmx to generate the topology. Could you share your ideas about this process ? What should I do ? You would just do everything the same way as setting up a new simulation and use the last frame as starting structure. Make sure you use a structure which includes both coordinates and velocities. Is there a way to get a tpr file from NAMD files? No. Not automatically. You need to get all the input files (grompp.mdp, topol.top, conf.gro) and then run grompp to generate your tpr. Roland Kind regards. Oguz GURBULAK Ph.D. Student Ege University - Faculty of Science Department of Physics Branch of Atomic and Molecular Physics -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] the density of liquid benzene is too large
Hello all, I am simulating liquid benzene. Initially, I generate a cubic box with 600 benzene molecules in it. The length of the box is 4.6 nm. Then I do the energy minimization and a NPT simulation for 20 ns. The force field I used for benzene is OPLSAA (JACS,1990,112,4768). And here is my .mdp file for the NPT simulation. title = benz cpp = /usr/bin/cpp define = integrator = md dt = 0.002; ps ! nsteps = 1000 comm_mode = Linear comm_grps = System nstxout = 0 nstvout = 2500 nstlog = 500 nstenergy = 50 nstxtcout = 500 nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 DispCorr= EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tcoupl = nose-hoover ref_t = 300 tau_t = 0.5 tc_grps = System pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 3.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 175298 constraints = hbonds constraint_algorithm= LINCS ;shake_tol = 0.0001 lincs_order = 4 lincs_iter = 1 To my surprise, the density of the system is too large to the experimental value (0.874 g/cm^3). Here are some results from the g_energy command. Statistics over 751 steps [ 5000. through 2. ps ], 8 data sets All statistics are over 750001 points Energy Average Err.Est. RMSD Tot-Drift --- Potential 13996.9 15302.701 -83.3695 (kJ/mol) Temperature 299.9760.000213.38239 -0.000582958 (K) Pressure1.08499 0.00721812.66 -0.026224 (bar) Box-X 4.334320.00086 0.0102765 -0.00488475 (nm) Box-Y 4.334320.00086 0.0102765 -0.00488475 (nm) Box-Z 4.334320.00086 0.0102765 -0.00488475 (nm) Volume 81.4276 0.049 0.579125 -0.275291 (nm^3) Density 955.828 0.576.800243.23201 (kg/m^3) Why the density is so large ? Could anyone give me some suggestions? Thank you in advance! Sincerely Cenfeng Fu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] cholesterol
Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. Thanks with best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Synthesis of Polyethylene SUrface Topology
Hi, I am a new user of GROMACS and I wish to Generate a Polyethylene Surface for my work related to hydrophobic Surface Properties. I went through an earlier available correspondencehttp://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.htmland tried to use the info available. After execution of pdb2gmx command and opting for OPLS force field, I got an error as: * Fatal error: Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms while sorting atoms * I am unable to understand the relevance of this error as in Polyethylene, Alcoholic group is not present whatsoever. Please help me in removing this particular error. -- Yash Gandhi, 4th Year, BE (Hons) Chemical, Birla Institute of Technology Science, Pilani, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] xpm file
Hi everyone, Please I need some help visualizing an .xpm file. I tried to open my .xpm file (g_hbond matrix) with Gimp but It gives me red lines that I don't understand. So I converted my .xpm file into an .eps file with xpm2ps. When I try to open my .eps file, I get the legend: Hydrogen bonds white=none red=Present And the legend of my axis: x axis=time(ps) y axis=Hydrogen Bond index But I can't see the values: It means I see that there is an axis but it's a black bold line instead of values of time or number of atoms in hydrogen bonds. Please how can I visualize correctly my matrix? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Synthesis of Polyethylene SUrface Topology
Yash Gandhi wrote: Hi, I am a new user of GROMACS and I wish to Generate a Polyethylene Surface for my work related to hydrophobic Surface Properties. I went through an earlier available correspondence http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html and tried to use the info available. After execution of pdb2gmx command and opting for OPLS force field, I got an error as: / Fatal error: Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms while sorting atoms / I am unable to understand the relevance of this error as in Polyethylene, Alcoholic group is not present whatsoever. Please help me in removing this particular error. Did you make all the appropriate changes to the .rtp and .hdb files, as instructed in the link above? Right now, pdb2gmx thinks your residues are named EtOH (ethanol), so either your coordinate file is named wrong or you haven't added the necessary information to the database. -Justin -- Yash Gandhi, 4th Year, BE (Hons) Chemical, Birla Institute of Technology Science, Pilani, India -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] xpm file
Carla Jamous wrote: Hi everyone, Please I need some help visualizing an .xpm file. I tried to open my .xpm file (g_hbond matrix) with Gimp but It gives me red lines that I don't understand. So I converted my .xpm file into an .eps file with xpm2ps. When I try to open my .eps file, I get the legend: Hydrogen bonds white=none red=Present And the legend of my axis: x axis=time(ps) y axis=Hydrogen Bond index But I can't see the values: It means I see that there is an axis but it's a black bold line instead of values of time or number of atoms in hydrogen bonds. You're not going to get any numbers in this plot (aside from hydrogen bond indices). The matrix you're trying to plot is an existence matrix, a red pixel if the hydrogen bond is present, a white one if none is present. You can map which hydrogen bond is which from the hbond.ndx file. That is, once you get it rendered properly (see below). Please how can I visualize correctly my matrix? You can alter its properties (proportions, x/y spacing) with a .m2p file. There is an example in the online manual. If the plot is simply a straight line, you'll probably want to decrease the x-spacing and increase the y-spacing to make it look normal. -Justin Thank you Carla -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] cholesterol
#ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the density of liquid benzene is too large
Cenfeng Fu wrote: Hello all, I am simulating liquid benzene. Initially, I generate a cubic box with 600 benzene molecules in it. The length of the box is 4.6 nm. Then I do the energy minimization and a NPT simulation for 20 ns. The force field I used for benzene is OPLSAA (JACS,1990,112,4768). And here is my .mdp file for the NPT simulation. title = benz cpp = /usr/bin/cpp define = integrator = md dt = 0.002; ps ! nsteps = 1000 comm_mode = Linear comm_grps = System nstxout = 0 nstvout = 2500 nstlog = 500 nstenergy = 50 nstxtcout = 500 nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 DispCorr= EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes tcoupl = nose-hoover ref_t = 300 tau_t = 0.5 tc_grps = System pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 3.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp= 300 gen_seed= 175298 constraints = hbonds constraint_algorithm= LINCS ;shake_tol = 0.0001 lincs_order = 4 lincs_iter = 1 To my surprise, the density of the system is too large to the experimental value (0.874 g/cm^3). Here are some results from the g_energy command. Statistics over 751 steps [ 5000. through 2. ps ], 8 data sets All statistics are over 750001 points Energy Average Err.Est. RMSD Tot-Drift --- Potential 13996.9 15302.701 -83.3695 (kJ/mol) Temperature 299.9760.000213.38239 -0.000582958 (K) Pressure1.08499 0.00721812.66 -0.026224 (bar) Box-X 4.334320.00086 0.0102765 -0.00488475 (nm) Box-Y 4.334320.00086 0.0102765 -0.00488475 (nm) Box-Z 4.334320.00086 0.0102765 -0.00488475 (nm) Volume 81.4276 0.049 0.579125 -0.275291 (nm^3) Density 955.828 0.576.800243.23201 (kg/m^3) Why the density is so large ? Could anyone give me some suggestions? Several possible reasons: 1. The force field parameters aren't perfect, so there is some inherent disagreement between simulation and reality. What is the expected value for this force field? 2. You're using the isothermal compressibility for water. If your system is pure liquid benzene, I'd think you would want to use the compressibility for benzene. I don't know how big the difference would be off-hand, but at least you'd be convinced that your simulation was set up properly. 3. Although it won't matter a huge amount, to what temperature does the experimental density correspond? Usually these parameters are given at 25C (298 K). The temperature you've used is 300 K. Again, a minor point, but one worth doing correctly in a simulation even though the such a change would not account for the magnitude of difference you're currently seeing. -Justin Thank you in advance! Sincerely Cenfeng Fu -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] charmm c36 lipids
Hello Sven, Drew and gmx-users, I've gotten requests from users that want to use the c36 CHARMM lipids in GROMACS (see below). So I answer both of you and the rest of the community in this e-mail. I have a script that parses the top and par files of CHARMM force field(s). It's not the most general piece of code there is so it will not be able to convert files that do not follow the format the CHARMM top and par files had when I wrote it (version c32b1). Also, it cannot parse the toppar files (i.e. what's called the toppar stream files in CHARMM). I downloaded the force field from: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz My script is able to parse the top_lipid_all36.rtf and par_all36_lipid.prm files without any errors and generate the corresponding GROMACS rtp, atp, bonded and nonbonded files. I'm not an CHARMM expert but if they haven't changed the force field considerable lately (by changing parameter definitions and functional forms of the force field for example) the files generated by the script should be the correct GROMACS translation. However, I cannot guarantee that all went well so I would suggest that those of you who are interested in this look through the files and convince yourself that the script did the job before running production runs with these parameters. I've put it on the old (and outdated) port homepage (http://www.dbb.su.se/User:Bjelkmar/Ffcharmm) so that those of you who are interested in this can access and test it. If nothing seems to be wrong after some of you have tested it I'm going to add it to the user contributions on gromacs.org. Regards, Pär Bjelkmar 1 okt 2010 kl. 09.53 skrev Sven Jakobtorweihen: Dear Pär Bjelkmar, thanks for implementing the CHARMM force field into GROMACS, that is really useful. Recently the CHARMM developers have introduced an updated lipid force field CHARMM36 for lipids, see Klauda et al. J. Phys. Chem. B, 2010, 114, 7830 (doi: 10.1021/jp101759q). It seems that this is an important improvement over the preceding version. I checked gromacs version 4.5.1 and the git-repository; unfortunately, the charmm36 lipids are not yet available in gromacs. However, I could write some scripts to convert the charmm files to gromacs files, I have the feeling the bonded parameter conversion is straight forward (having the charmm27 files for gromacs), but I fear that transferring the bonded parameters is tedious. So my question is: Do you have by any change already gromacs files for charmm36 lipids? Or are scripts available to convert charmm FF to gromacs FF files? I am aware of the charmm_to_gromacs perl scripts on the gromacs website. But as fare as I know they are not compatible with the official implementation of charmm in gromacs, or am I wrong? Thanks for your help. Best regards, Sven -- * Dr.-Ing. Sven Jakobtorweihen Hamburg University of Technology Institute of Chemical Reaction Engineering / V2 Eissendorfer Str. 38 21073 Hamburg Germany PHONE : ++49 (0) 40 42878 2491 FAX : ++49 (0) 40 42878 2145 E-MAIL: jakobtorwei...@tuhh.de * 3 sep 2010 kl. 20.56 skrev Drew Bennett: Dear Pr Bjelkmar, I saw on the gromacs mailing list that you have python a script for converting CHARMM ff to GMX. I would greatly appreciate if you could please send it to me. I am trying to use the new CHARMM36 lipids for a simulation with a membrane protein. Thank-you. Drew Bennett -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] cholesterol
Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] charmm c36 lipids
Hi Par, I have a working version of the CHARMM36 lipids that I converted myself, which I am fairly confident is correct. I shall check your parameters against my ones to confirm everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. Cheers Tom Pär Bjelkmar wrote: Hello Sven, Drew and gmx-users, I've gotten requests from users that want to use the c36 CHARMM lipids in GROMACS (see below). So I answer both of you and the rest of the community in this e-mail. I have a script that parses the top and par files of CHARMM force field(s). It's not the most general piece of code there is so it will not be able to convert files that do not follow the format the CHARMM top and par files had when I wrote it (version c32b1). Also, it cannot parse the toppar files (i.e. what's called the toppar stream files in CHARMM). I downloaded the force field from: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz My script is able to parse the top_lipid_all36.rtf and par_all36_lipid.prm files without any errors and generate the corresponding GROMACS rtp, atp, bonded and nonbonded files. I'm not an CHARMM expert but if they haven't changed the force field considerable lately (by changing parameter definitions and functional forms of the force field for example) the files generated by the script should be the correct GROMACS translation. However, I cannot guarantee that all went well so I would suggest that those of you who are interested in this look through the files and convince yourself that the script did the job before running production runs with these parameters. I've put it on the old (and outdated) port homepage (http://www.dbb.su.se/User:Bjelkmar/Ffcharmm) so that those of you who are interested in this can access and test it. If nothing seems to be wrong after some of you have tested it I'm going to add it to the user contributions on gromacs.org http://gromacs.org. Regards, Pär Bjelkmar 1 okt 2010 kl. 09.53 skrev Sven Jakobtorweihen: Dear Pär Bjelkmar, thanks for implementing the CHARMM force field into GROMACS, that is really useful. Recently the CHARMM developers have introduced an updated lipid force field CHARMM36 for lipids, see Klauda et al. J. Phys. Chem. B, 2010, 114, 7830 (doi: 10.1021/jp101759q). It seems that this is an important improvement over the preceding version. I checked gromacs version 4.5.1 and the git-repository; unfortunately, the charmm36 lipids are not yet available in gromacs. However, I could write some scripts to convert the charmm files to gromacs files, I have the feeling the bonded parameter conversion is straight forward (having the charmm27 files for gromacs), but I fear that transferring the bonded parameters is tedious. So my question is: Do you have by any change already gromacs files for charmm36 lipids? Or are scripts available to convert charmm FF to gromacs FF files? I am aware of the charmm_to_gromacs perl scripts on the gromacs website. But as fare as I know they are not compatible with the official implementation of charmm in gromacs, or am I wrong? Thanks for your help. Best regards, Sven -- * Dr.-Ing. Sven Jakobtorweihen Hamburg University of Technology Institute of Chemical Reaction Engineering / V2 Eissendorfer Str. 38 21073 Hamburg Germany PHONE : ++49 (0) 40 42878 2491 FAX : ++49 (0) 40 42878 2145 E-MAIL: jakobtorwei...@tuhh.de mailto:jakobtorwei...@tuhh.de * 3 sep 2010 kl. 20.56 skrev Drew Bennett: Dear Pr Bjelkmar, I saw on the gromacs mailing list that you have python a script for converting CHARMM ff to GMX. I would greatly appreciate if you could please send it to me. I am trying to use the new CHARMM36 lipids for a simulation with a membrane protein. Thank-you. Drew Bennett -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] cholesterol
#ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] cholesterol
Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] cholesterol
I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] cholesterol
Thanks for your clue. I found the very interesting paper about that force field. Thanks again, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Piggot [t.pig...@soton.ac.uk] Sent: Friday, October 01, 2010 9:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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.
Re: [gmx-users] charmm c36 lipids
Hi Tom, great do that! If there're no discrepancies and you have tested it we should probably put your version among the user contributions. Let me know how it goes! /Pär Hi Par, I have a working version of the CHARMM36 lipids that I converted myself, which I am fairly confident is correct. I shall check your parameters against my ones to confirm everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] charmm c36 lipids
Hello, I also had the opportunity to import and test the CHARMM36 lipids with Gromacs. There is not particular issue with those lipids and I guess any script able to convert charmm27 topology and parameter files in Gromacs file should work with charmm36. Nico Hi Par, I have a working version of the CHARMM36 lipids that I converted myself, which I am fairly confident is correct. I shall check your parameters against my ones to confirm everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. Cheers Tom Pär Bjelkmar wrote: Hello Sven, Drew and gmx-users, I've gotten requests from users that want to use the c36 CHARMM lipids in GROMACS (see below). So I answer both of you and the rest of the community in this e-mail. I have a script that parses the top and par files of CHARMM force field(s). It's not the most general piece of code there is so it will not be able to convert files that do not follow the format the CHARMM top and par files had when I wrote it (version c32b1). Also, it cannot parse the toppar files (i.e. what's called the toppar stream files in CHARMM). I downloaded the force field from: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz My script is able to parse the top_lipid_all36.rtf and par_all36_lipid.prm files without any errors and generate the corresponding GROMACS rtp, atp, bonded and nonbonded files. I'm not an CHARMM expert but if they haven't changed the force field considerable lately (by changing parameter definitions and functional forms of the force field for example) the files generated by the script should be the correct GROMACS translation. However, I cannot guarantee that all went well so I would suggest that those of you who are interested in this look through the files and convince yourself that the script did the job before running production runs with these parameters. I've put it on the old (and outdated) port homepage (http://www.dbb.su.se/User:Bjelkmar/Ffcharmm) so that those of you who are interested in this can access and test it. If nothing seems to be wrong after some of you have tested it I'm going to add it to the user contributions on gromacs.org http://gromacs.org. Regards, Pär Bjelkmar 1 okt 2010 kl. 09.53 skrev Sven Jakobtorweihen: Dear Pär Bjelkmar, thanks for implementing the CHARMM force field into GROMACS, that is really useful. Recently the CHARMM developers have introduced an updated lipid force field CHARMM36 for lipids, see Klauda et al. J. Phys. Chem. B, 2010, 114, 7830 (doi: 10.1021/jp101759q). It seems that this is an important improvement over the preceding version. I checked gromacs version 4.5.1 and the git-repository; unfortunately, the charmm36 lipids are not yet available in gromacs. However, I could write some scripts to convert the charmm files to gromacs files, I have the feeling the bonded parameter conversion is straight forward (having the charmm27 files for gromacs), but I fear that transferring the bonded parameters is tedious. So my question is: Do you have by any change already gromacs files for charmm36 lipids? Or are scripts available to convert charmm FF to gromacs FF files? I am aware of the charmm_to_gromacs perl scripts on the gromacs website. But as fare as I know they are not compatible with the official implementation of charmm in gromacs, or am I wrong? Thanks for your help. Best regards, Sven -- * Dr.-Ing. Sven Jakobtorweihen Hamburg University of Technology Institute of Chemical Reaction Engineering / V2 Eissendorfer Str. 38 21073 Hamburg Germany PHONE : ++49 (0) 40 42878 2491 FAX : ++49 (0) 40 42878 2145 E-MAIL: jakobtorwei...@tuhh.de mailto:jakobtorwei...@tuhh.de * 3 sep 2010 kl. 20.56 skrev Drew Bennett: Dear Pr Bjelkmar, I saw on the gromacs mailing list that you have python a script for converting CHARMM ff to GMX. I would greatly appreciate if you could please send it to me. I am trying to use the new CHARMM36 lipids for a simulation with a membrane protein. Thank-you. Drew Bennett -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44/53 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] charmm c36 lipids
Hi Par, For a POPC bilayer then both your and my files produce the same tpr's (checked both with gmxcheck and gmxdump). This is pleasing as I not only scripted the conversions but did some parts by hand! I shall check the other lipids to make sure that there are no discrepancies in these. Also for my files I have included the bonded and non-bonded parameters with parameters from CHARMM27 so as to allow simulations in water and with proteins. I want to re-check these before contributing the forcefield to the website, so it will probably be next week before I upload it. Just to let you know I will use your lipids.rtp as it has the atoms in separate charge groups so as to avoid having to use -nochargegrp with pdb2gmx, whilst mine doesn't. I hope this is fine with you. Cheers Tom Pär Bjelkmar wrote: Hi Tom, great do that! If there're no discrepancies and you have tested it we should probably put your version among the user contributions. Let me know how it goes! /Pär Hi Par, I have a working version of the CHARMM36 lipids that I converted myself, which I am fairly confident is correct. I shall check your parameters against my ones to confirm everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Another error that keeps comming up.
On October 1, 2010 at 2:37 AM Roland Schulz rol...@utk.edu wrote: After how many steps do you get the error? Do you get the error also with -dlb yes and theenvironmentvariableGMX_DLB_FLOP set to 1 or 2? Thank you for your interest but I think I found the issue. I am using a cluster I built with many different computers. All have 3.04 GHz pentium 4 processors but the other components vary. I have since recompiled GROMACS 4.5.1 on each computer separately (albeit a tedious task but well worth it). Now I am running smooth and have become a preacher of this individual gromacs compiling. Below is what occurred before the fix The error would occur at random number of stems but never above 5000. It was very intermittent and I believe this to be the jobs node selection. If a job ran on one node it would work and on another it would not. I came to the conclusion above by running the jobs that failed on my workstation which of course had gromacs compiled on it rather than on another machine. I just hope that this post will save the next guy some heartache and precious time. Thank you again, TJ Mustard Roland On Tue, Sep 28, 2010 at 12:54 PM, TJ Mustard musta...@onid.orst.edu wrote: Found that if I set the setting of -dlb no when running the mdrun it would not fail. How could dynamic load balancing do this? TJ Mustard On September 28, 2010 at 3:21 AM TJ Mustard musta...@onid.orst.edu wrote: Hey all, Here is another error that I keep getting. I am trying to speed up my md runs with -heavyh and longer time steps. I dont get LINCS errors but I do get this... Back Off! I just backed up prlog.log to ./#prlog.log.1# Getting Loaded... Reading file monomer_pr.tpr, VERSION 4.5.1 (single precision) Starting 2 threads Loaded with Money Making 1D domain decomposition 2 x 1 x 1 Back Off! I just backed up pr.edr to ./#pr.edr.1# starting mdrun Protein in water 25000 steps, 100.0 ps. step 900, will finish Mon Sep 27 18:19:07 2010imb F 18% NOTE: Turning on dynamic load balancing step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92 imb F 1% A list of missing interactions: LJC Pairs NB of 278 missing 1 exclusions of 6966 missing 1 --- Program g4.5.1-mdrun, VERSION 4.5.1 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Some settings: define = -DPOSRES dt = 0.004 nsteps = 25000 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME ; = Cutoff rcoulomb-switch = 0 ; = 0 rcoulomb = 0.9 ; = 1 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 ; = 1 epsilon_rf = 1 ; = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; = Cut-off ; cut-off lengths rvdw-switch = 0 ; = 0 rvdw = 1 ; = 1 ; Apply long range dispersion
[gmx-users] Is there a setting for defualt genion selection?
Hello all, Is there a argument that will select SOL as the defualt selection for ion substitution? I read the manual and found nothing. Thank you, TJ Mustard Email: musta...@onid.orst.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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Is there a setting for defualt genion selection?
TJ Mustard wrote: Hello all, Is there a argument that will select SOL as the defualt selection for ion substitution? I read the manual and found nothing. No, but if you're trying to incorporate this into a script or something, see: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Thank you, TJ Mustard Email: musta...@onid.orst.edu -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Is GROMACS right for 2-D Potential?
Dear all, I want to simulate nitric oxide, with fixed bond length, in liquid argon. I have the Ar-NO potential from ab initio quantum mechanical calcullations as a function of Jacobi coordinates, r and theta, where r is the vector locating the Ar from the center of mass of NO and theta is the angle between the bond vector and the vector r. I have made fits to these models which are V(r, theta)=(exponential terms(r) + V_Lennard Jones(r))*Legendre Polynomial(theta). It is very easy to make a look up table for this potential but it is a function of two coordinates, either r and theta, or the r1 and r2 where r1 is the distance between the Ar and O and r2 is the distance between the Ar and N. Can anyone point me in the right direction for getting started on the force field I should use to simulate this system or how to code a splined look up table? Thank you very much for your time, - Mick Warehime University of Maryland -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Is there a setting for defualt genion selection?
On October 1, 2010 at 7:16 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: Hello all, Is there a argument that will select SOL as the defualt selection for ion substitution? I read the manual and found nothing. No, but if youre trying to incorporate this into a script or something, see: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Perfect thank you. TJ Mustard Thank you, TJ Mustard Email: musta...@onid.orst.edu -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] gromacs synaptic package manager
Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? Thanks a lot for any instruction. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gromacs synaptic package manager
ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? If I were you, I would uninstall this version (which is outdated by nearly 2 years!) and get version 4.5.1. Installing from source is quite easy. Not only will you benefit from hundreds of bug fixes and enhancements, but running in parallel on a multi-core machine is no longer MPI-dependent, making it somewhat easier. For usage and instructions, see the manual and any of the numerous tutorials linked here: http://www.gromacs.org/Documentation/Tutorials#General -Justin Thanks a lot for any instruction. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gromacs synaptic package manager
Dear justin, Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed it. I enter this line a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install in terminal. What can I do? I am sorry. I am a new user. Thanks in advance 1. I installed fftw 3.2.2 a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install 2. I tried to install Gromacs 4.5.1 a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install Making install in include make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' Making install in . make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Nothing to be done for `install-exec-am'. test -z /usr/local/gromacs/include/gromacs || /bin/mkdir -p /usr/local/gromacs/include/gromacs /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make: *** [install-recursive] Error 1 2010/10/1 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? If I were you, I would uninstall this version (which is outdated by nearly 2 years!) and get version 4.5.1. Installing from source is quite easy. Not only will you benefit from hundreds of bug fixes and enhancements, but running in parallel on a multi-core machine is no longer MPI-dependent, making it somewhat easier. For usage and instructions, see the manual and any of the numerous tutorials linked here: http://www.gromacs.org/Documentation/Tutorials#General -Justin Thanks a lot for any instruction. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gromacs synaptic package manager
Hi, either install as root by running: sudo make install or rerun the installation steps with ./configure --prefix=$HOME/usr to install it in your home directory. Roland 2010/10/1 ahmet yıldırım ahmedo...@gmail.com Dear justin, Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed it. I enter this line a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install in terminal. What can I do? I am sorry. I am a new user. Thanks in advance 1. I installed fftw 3.2.2 a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install 2. I tried to install Gromacs 4.5.1 a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install Making install in include make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' Making install in . make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Nothing to be done for `install-exec-am'. test -z /usr/local/gromacs/include/gromacs || /bin/mkdir -p /usr/local/gromacs/include/gromacs /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make: *** [install-recursive] Error 1 2010/10/1 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? If I were you, I would uninstall this version (which is outdated by nearly 2 years!) and get version 4.5.1. Installing from source is quite easy. Not only will you benefit from hundreds of bug fixes and enhancements, but running in parallel on a multi-core machine is no longer MPI-dependent, making it somewhat easier. For usage and instructions, see the manual and any of the numerous tutorials linked here: http://www.gromacs.org/Documentation/Tutorials#General -Justin Thanks a lot for any instruction. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gromacs synaptic package manager
Dear Roland, Eventually I installed the installation steps with ./configure --prefix=$HOME/usr as you said. can you send me the input file for test? I want to run a simulation. how can I do this? Thanks for your helps 2010/10/2 Roland Schulz rol...@utk.edu Hi, either install as root by running: sudo make install or rerun the installation steps with ./configure --prefix=$HOME/usr to install it in your home directory. Roland 2010/10/1 ahmet yıldırım ahmedo...@gmail.com Dear justin, Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed it. I enter this line a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install in terminal. What can I do? I am sorry. I am a new user. Thanks in advance 1. I installed fftw 3.2.2 a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install 2. I tried to install Gromacs 4.5.1 a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install Making install in include make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' Making install in . make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Nothing to be done for `install-exec-am'. test -z /usr/local/gromacs/include/gromacs || /bin/mkdir -p /usr/local/gromacs/include/gromacs /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make: *** [install-recursive] Error 1 2010/10/1 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? If I were you, I would uninstall this version (which is outdated by nearly 2 years!) and get version 4.5.1. Installing from source is quite easy. Not only will you benefit from hundreds of bug fixes and enhancements, but running in parallel on a multi-core machine is no longer MPI-dependent, making it somewhat easier. For usage and instructions, see the manual and any of the numerous tutorials linked here: http://www.gromacs.org/Documentation/Tutorials#General -Justin Thanks a lot for any instruction. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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
Re: [gmx-users] gromacs synaptic package manager
As Justin said: Look at one of the many tutorials. Roland 2010/10/1 ahmet yıldırım ahmedo...@gmail.com Dear Roland, Eventually I installed the installation steps with ./configure --prefix=$HOME/usr as you said. can you send me the input file for test? I want to run a simulation. how can I do this? Thanks for your helps 2010/10/2 Roland Schulz rol...@utk.edu Hi, either install as root by running: sudo make install or rerun the installation steps with ./configure --prefix=$HOME/usr to install it in your home directory. Roland 2010/10/1 ahmet yıldırım ahmedo...@gmail.com Dear justin, Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed it. I enter this line a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install in terminal. What can I do? I am sorry. I am a new user. Thanks in advance 1. I installed fftw 3.2.2 a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install 2. I tried to install Gromacs 4.5.1 a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install Making install in include make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' Making install in . make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Nothing to be done for `install-exec-am'. test -z /usr/local/gromacs/include/gromacs || /bin/mkdir -p /usr/local/gromacs/include/gromacs /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make: *** [install-recursive] Error 1 2010/10/1 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? If I were you, I would uninstall this version (which is outdated by nearly 2 years!) and get version 4.5.1. Installing from source is quite easy. Not only will you benefit from hundreds of bug fixes and enhancements, but running in parallel on a multi-core machine is no longer MPI-dependent, making it somewhat easier. For usage and instructions, see the manual and any of the numerous tutorials linked here: http://www.gromacs.org/Documentation/Tutorials#General -Justin Thanks a lot for any instruction. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please
Re: [gmx-users] gromacs synaptic package manager
ahmet yıldırım wrote: Dear Roland, Eventually I installed the installation steps with ./configure --prefix=$HOME/usr as you said. can you send me the input file for test? I want to run a simulation. how can I do this? Please do some tutorial material. I sent you the link before. -Justin Thanks for your helps 2010/10/2 Roland Schulz rol...@utk.edu mailto:rol...@utk.edu Hi, either install as root by running: sudo make install or rerun the installation steps with ./configure --prefix=$HOME/usr to install it in your home directory. Roland 2010/10/1 ahmet yıldırım ahmedo...@gmail.com mailto:ahmedo...@gmail.com Dear justin, Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed it. I enter this line a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install in terminal. What can I do? I am sorry. I am a new user. Thanks in advance 1. I installed fftw 3.2.2 a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install 2. I tried to install Gromacs 4.5.1 a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install Making install in include make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' Making install in . make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[3]: Nothing to be done for `install-exec-am'. test -z /usr/local/gromacs/include/gromacs || /bin/mkdir -p /usr/local/gromacs/include/gromacs /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make: *** [install-recursive] Error 1 2010/10/1 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? If I were you, I would uninstall this version (which is outdated by nearly 2 years!) and get version 4.5.1. Installing from source is quite easy. Not only will you benefit from hundreds of bug fixes and enhancements, but running in parallel on a multi-core machine is no longer MPI-dependent, making it somewhat easier. For usage and instructions, see the manual and any of the numerous tutorials linked here: http://www.gromacs.org/Documentation/Tutorials#General -Justin Thanks a lot for any instruction. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
