[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL
Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would take the usual place of solvent within a binding region or other solvent accessible surface and it might be more realistic to simulate the ligand as part of the solvent's ensemble (one might run two simulations in order to compare the ligand-protein interaction to the water-protein interaction at the interaction interface...) -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] rationale behind tcoupling ligand with protein instead of with SOL
Hi peter I think the important is to don't couple small number of atoms(ligand molecules or a few ions) separately to a reference tempreture! It probably will result the same if you make two tcouple groups as below: Protein-LIG water-ions or Proteinwater-ions-LIG I think they will be equvalent( with a good approximation)! On Mon, Apr 11, 2011 at 10:32 AM, Peter C. Lai p...@uab.edu wrote: Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would take the usual place of solvent within a binding region or other solvent accessible surface and it might be more realistic to simulate the ligand as part of the solvent's ensemble (one might run two simulations in order to compare the ligand-protein interaction to the water-protein interaction at the interaction interface...) -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] rationale behind tcoupling ligand with protein instead of with SOL
Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would take the usual place of solvent within a binding region or other solvent accessible surface and it might be more realistic to simulate the ligand as part of the solvent's ensemble (one might run two simulations in order to compare the ligand-protein interaction to the water-protein interaction at the interaction interface...) Might depend how enclosed the binding pocket is, and whether things are moving. The rate of inter-group heat flow (roughly) depends on the surface area, and it's rational to group the ligand with the group that has the larger relevant surface area in contact with the ligand. 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/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] problem with mpiexec, mdrun in gromacs/4.0.7
Hello I want to run a simulation in gromacs/4.0.7 because this version supports v-rescale option for thermostat and I need that. tcoupl=v-rescale in this version the grompp command does not need -np option. please let me know how I can specify the number of processors for my job. I use a .ll file to submit my job. in this file the command line is: mpiexec mdrun_mpi -v -s topol.tpr -np 8 (this is a coomand line which I used previously in my .ii file for gromacs/3.3 is this command line suitable for version 4/0/7 as well or I should change something? Thanks in advance D.Aghaie --- On Fri, 4/8/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] unable to equilibrate protein in membrane with NPT To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, April 8, 2011, 5:32 PM Peter C. Lai wrote: Hello again In my protein-membrane-water-ion system (inserted via g_membed) I have run a 1ns NVT equilibration with the protein restrained and now I am trying to equilibrate with NPT and LINCS/mdrun is crashing after about 5000 iterations. Here is my NPT mdp file: define =-DPOSRES integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 50 init_step = 0 comm-mode = Linear nstcomm = 1 comm-grps = Protein_POPC SOL_CL nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT tcoupl = Nose-Hoover tc-grps = Protein POPC SOL_CL tau-t = 0.5 0.5 0.5 ref-t = 300 300 300 gen-vel = no pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; tau_p = 5.0 ; time constant, in ps ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 Any suggestions? Try using the Berendsen barostat. P-R allows for wider oscillations that can lead to instability in incompletely equilibrated systems. -Justin -- 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 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] rationale behind tcoupling ligand with protein instead of with SOL
On 2011-04-11 01:24:49AM -0500, Mark Abraham wrote: Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would take the usual place of solvent within a binding region or other solvent accessible surface and it might be more realistic to simulate the ligand as part of the solvent's ensemble (one might run two simulations in order to compare the ligand-protein interaction to the water-protein interaction at the interaction interface...) Might depend how enclosed the binding pocket is, and whether things are moving. The rate of inter-group heat flow (roughly) depends on the surface area, and it's rational to group the ligand with the group that has the larger relevant surface area in contact with the ligand. hmm Well my binding pocket also has water diffusing into it, and some of them get replaced by the ligand atoms during binding, that's why I figured the ligand should be heated with the same bath as the water, since it would also be interesting to look at the interaction between any leftover water and the ligand...(and the water should be in motion over a simulation even though there are only a few [ 20 ] of them...I did not assign binding pocket waters to the protein bath because I do not know the diffusion rate and did not think it would be good to have them moving at different average velocity distribution compared to the outside water since theoretically they should be interchangeable...). The way the ligand was docked was that I emptied out the binding pocket, docked the ligand, then I took the ligand coordinates the docking program gave me and put it into the unbound ligand, then removed any overlapping waters, sort of how g_membed inserts the a protein into the bilayer. I guess I can run both cases and see what happens... 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/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 -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] problem with mpiexec, mdrun in gromacs/4.0.7
Hello I want to run a simulation in gromacs/4.0.7 because this version supports v-rescale option for thermostat and I need that. tcoupl=v-rescale Do the job properly, and install 4.5.4 for better parallel performance and more bug fixes. *in this version the grompp command does not need -np option. please let me know how I can specify the number of processors for my job.* See http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp#Parallel_calculations I use a *.ll* file to submit my job. in this file the command line is: *mpiexec mdrun_mpi -v -s topol.tpr -np 8* (this is a coomand line which I used previously in my .ii file for gromacs/3.3 is this command line suitable for version 4/0/7 as well or I should change something? It will work in 4.0.7 and 4.5.4 using all the processors available to mpiexec, and the -np 8 is ignored. Mark Thanks in advance D.Aghaie --- On *Fri, 4/8/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] unable to equilibrate protein in membrane with NPT To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, April 8, 2011, 5:32 PM Peter C. Lai wrote: Hello again In my protein-membrane-water-ion system (inserted via g_membed) I have run a 1ns NVT equilibration with the protein restrained and now I am trying to equilibrate with NPT and LINCS/mdrun is crashing after about 5000 iterations. Here is my NPT mdp file: define =-DPOSRES integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 50 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= Protein_POPC SOL_CL nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation= yes constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT tcoupl = Nose-Hoover tc-grps = Protein POPC SOL_CL tau-t= 0.5 0.5 0.5 ref-t= 300 300 300 gen-vel = no pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; tau_p = 5.0 ; time constant, in ps ref_p = 1.01325 1.01325 compressibility = 4.5e-54.5e-5 Any suggestions? Try using the Berendsen barostat. P-R allows for wider oscillations that can lead to instability in incompletely equilibrated systems. -Justin -- 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://us.mc1301.mail.yahoo.com/mc/compose?to=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 http://us.mc1301.mail.yahoo.com/mc/compose?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
Re: [gmx-users] rationale behind tcoupling ligand with protein instead of with SOL
On 2011-04-11 01:24:49AM -0500, Mark Abraham wrote: Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would take the usual place of solvent within a binding region or other solvent accessible surface and it might be more realistic to simulate the ligand as part of the solvent's ensemble (one might run two simulations in order to compare the ligand-protein interaction to the water-protein interaction at the interaction interface...) Might depend how enclosed the binding pocket is, and whether things are moving. The rate of inter-group heat flow (roughly) depends on the surface area, and it's rational to group the ligand with the group that has the larger relevant surface area in contact with the ligand. hmm Well my binding pocket also has water diffusing into it, and some of them get replaced by the ligand atoms during binding, that's why I figured the ligand should be heated with the same bath as the water, since it would also be interesting to look at the interaction between any leftover water and the ligand...(and the water should be in motion over a simulation even though there are only a few [20 ] of them...I did not assign binding pocket waters to the protein bath because I do not know the diffusion rate and did not think it would be good to have them moving at different average velocity distribution compared to the outside water since theoretically they should be interchangeable...). The way the ligand was docked was that I emptied out the binding pocket, docked the ligand, then I took the ligand coordinates the docking program gave me and put it into the unbound ligand, then removed any overlapping waters, sort of how g_membed inserts the a protein into the bilayer. Yeah, that sort of stuff is why I was hedging with relevant surface area. Mark I guess I can run both cases and see what happens... 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/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
[gmx-users] Re : Simulation for prediction of binding between a peptide and protein
Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@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/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] comm-grps for a membrane-protein-ligand system
Peter C. Lai wrote: Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correction vector applied to both relative to SOL_Ions but I just wanted to make sure... If specifying multiple groups for COM motion removal, yes, the intuitive solution is to group the ligand with the protein (since they're physically bound, presumably). The general complication is whether or not multiple COM groups are necessary - if the protein protrudes out into the solvent in any substantial way, you could have instability when the solvent and protein/membrane COMs get re-set. I have seen this before in the case of a protein in water with separate COM groups (which is not appropriate, for the record). Membrane systems are somewhat more complicated because they form interfaces that can slide, but if the protein somehow affects this behavior, well, I don't know that there's a trivial solution other than comm_grps = System to avoid possible instability. If you're interested in diffusion-related properties, on the other hand, that may not be appropriate. Plenty to think about, but again, probably no easy solution. -Justin -- 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] Re : Simulation for prediction of binding between a peptide and protein
Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? I don't think anybody has the computational resources to answer this question with unguided MD. Docking programs are probably the way to get a guide about what binding modes might be reasonable, but I don't know what software might be fit for the purpose. 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/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] mdrun segmentation fault
Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions, 1:1 water: methanol (~3000 molecules of each) in 8 nm cube I had had EM of the system using steepest decent. Outcome: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.5354981e+19 Maximum force =inf on atom 651 Norm of force =inf *The minim.mdp *is: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.02 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none *The nvt.mdp*: title= hist NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002 ; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes; assign velocities from Maxwell distribution gen_temp = 300; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I tried to decrease the step size, that also runs into seg fault error. Kindly guide. Thanks, SN -- 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] mdrun segmentation fault
shivangi nangia wrote: Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions, 1:1 water: methanol (~3000 molecules of each) in 8 nm cube I had had EM of the system using steepest decent. Outcome: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.5354981e+19 Maximum force =inf on atom 651 Norm of force =inf You were already told that this is the source of your problem and any procedure is destined to fail. What's more, you were given hints on how to solve your issue: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060268.html -Justin -- 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] g_hbond
Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. I am using Gromacs 4.0.7 version. Nilesh -- 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] g_hbond
Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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] g_hbond
Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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] g_hbond
Nilesh Dhumal wrote: Is there any way to specify clorin and florin atoms as a receptor. Modify the code. -Justin Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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] rationale behind tcoupling ligand with protein instead of with SOL
You didn't state your usage, but if you're doing US or decoupling, etc (some method where you lose the dynamics anyway) I suggest that you use Langevin dynamics. You will get the correct ensemble. Separate temperature coupling groups is a trick that helps in some cases, but it still does not give you the correct ensemble. Chris. -- original message -- Any rationale behind the thermostat coupling of a ligand with the protein instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme binding example)? Especially with small drug-type molecules as generally the ligand might/would take the usual place of solvent within a binding region or other solvent accessible surface and it might be more realistic to simulate the ligand as part of the solvent's ensemble (one might run two simulations in order to compare the ligand-protein interaction to the water-protein interaction at the interaction interface...) -- 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] comm-grps for a membrane-protein-ligand system
Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen stability issues otherwise with COM turned on in the case of the unbound protein and the membrane as separate COM groups. The only instability I have encountered thus far is LINCS crashing due to too much forces if I set the restraint forces too high (like 10 kJ/mol), but I've resigned myself to the fact that the residual RMS drift appears acceptable at the end of membrane/solvent equilibration runs if I drop it down to 1 kJ/mol during NPT equilibration). On 2011-04-11 07:00:39AM -0500, Justin A. Lemkul wrote: Peter C. Lai wrote: Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correction vector applied to both relative to SOL_Ions but I just wanted to make sure... If specifying multiple groups for COM motion removal, yes, the intuitive solution is to group the ligand with the protein (since they're physically bound, presumably). The general complication is whether or not multiple COM groups are necessary - if the protein protrudes out into the solvent in any substantial way, you could have instability when the solvent and protein/membrane COMs get re-set. I have seen this before in the case of a protein in water with separate COM groups (which is not appropriate, for the record). Membrane systems are somewhat more complicated because they form interfaces that can slide, but if the protein somehow affects this behavior, well, I don't know that there's a trivial solution other than comm_grps = System to avoid possible instability. If you're interested in diffusion-related properties, on the other hand, that may not be appropriate. Plenty to think about, but again, probably no easy solution. -Justin -- 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 -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR
Dear community. I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4 but unfortunately the system showed configure: error: Cannot find fftw3 library after launch the ./configure (you can see below) Really I do not understand because I did before this: # export LDFLAGS=-L/opt/rocks/lib # export CPPFLAGS=-I/opt/rocks/include # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs configure: error: Cannot find fftw3 library I would be very grateful if someone could help me or give me advices. By the way... I am trying to reproduce the steps posted in http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/for compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 and the option --disable-float is not clear for me. Thank you in advance. Miguel Quiliano. P.S I attach the error # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... yes checking whether mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... mpicc -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld
Re: [gmx-users] comm-grps for a membrane-protein-ligand system
Peter C. Lai wrote: Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen There is no center to a periodic system. Molecules diffuse, there's no way around it. If you try to apply some biasing force to fit some visualization convenience, you're potentially damaging the simulation's integrity. stability issues otherwise with COM turned on in the case of the unbound protein and the membrane as separate COM groups. The only instability I have encountered thus far is LINCS crashing due to too much forces if I set the restraint forces too high (like 10 kJ/mol), but I've resigned myself to the fact that the residual RMS drift appears acceptable at the end of membrane/solvent equilibration runs if I drop it down to 1 kJ/mol during NPT equilibration). Position restraints do not fix anything in place, they merely provide an energy barrier that penalizes change. If your goal is simply to obtain a reasonably equilibrated system, then there is no need for a force constant above about 1000, otherwise you may be overtly influencing the ability of your system to respond to change. -Justin On 2011-04-11 07:00:39AM -0500, Justin A. Lemkul wrote: Peter C. Lai wrote: Should I couple a ligand associated with a membrane protein to the same COM group as the Protein_POPC group? It makes sense to me that would be the case since if we are investigating the interaction between protein+membrane and ligand we want to have the same COM correction vector applied to both relative to SOL_Ions but I just wanted to make sure... If specifying multiple groups for COM motion removal, yes, the intuitive solution is to group the ligand with the protein (since they're physically bound, presumably). The general complication is whether or not multiple COM groups are necessary - if the protein protrudes out into the solvent in any substantial way, you could have instability when the solvent and protein/membrane COMs get re-set. I have seen this before in the case of a protein in water with separate COM groups (which is not appropriate, for the record). Membrane systems are somewhat more complicated because they form interfaces that can slide, but if the protein somehow affects this behavior, well, I don't know that there's a trivial solution other than comm_grps = System to avoid possible instability. If you're interested in diffusion-related properties, on the other hand, that may not be appropriate. Plenty to think about, but again, probably no easy solution. -Justin -- 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] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR
Miguel Quiliano Meza wrote: Dear community. I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4 but unfortunately the system showed configure: error: Cannot find fftw3 library after launch the ./configure (you can see below) Really I do not understand because I did before this: # export LDFLAGS=-L/opt/rocks/lib # export CPPFLAGS=-I/opt/rocks/include # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs configure: error: Cannot find fftw3 library You have a precision mismatch. By using --disable-float you are trying to install Gromacs in double precision (which for most applications is not necessary and results in some performance loss). Thus, you need FFTW in double precision as well. You probably compiled FFTW in single precision, thus the libraries are named libfftw3f, not libfftw3. -Justin I would be very grateful if someone could help me or give me advices. By the way... I am trying to reproduce the steps posted in http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/ for compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 and the option --disable-float is not clear for me. Thank you in advance. Miguel Quiliano. P.S I attach the error # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... yes checking whether mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... mpicc -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking
Re: [gmx-users] g_hbond
Try the -contact option. Erik Nilesh Dhumal skrev 2011-04-11 17.12: Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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 -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Pressure coupling problem
Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for *Ethanol* using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again looks fine. When I started running the NVT script, I set it equal to a ref_T of 298 K. It equilibrated at the temperature. Then I tried using an NPT script to equilibrate it to a ref_p of 1 bar. This is where I get the problem. The output shows the density is close to the actual experimental value of 0.789 g/cm^3. But for some reason, my pressure never gets an average of 1 bar. It keeps oscillating, which I understand is normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002). I don't understand why the ref_p of 1 bar is not working when I run this NPT.mdp script file. My simple goal is to have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1 bar and somewhere near the experimental density. I would really appreciate anybody's help! I'm new to this but I'm eager to keep getting better. Thanks. *NVT SCRIPT (this works fine and takes me to 298 K)* File Edit Options Buffers Tools Help title =CHARMM ETHANOL NVT equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100;save coordinates every 0.2 ps nstvout =100;save velocities every 0.2 ps nstenergy =100;save energies every 0.2 ps nstlog =100;update log file every 0.2 ps ;Bond parameters continuation=no ;first dynamics run constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0;short-range neighborlist cutoff (in nm) rcoulomb=1.0;short-range electrostatic cutoff (in nm) rvdw=1.0;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT ;Temperature coupling is on tcoupl =V-rescale ;modified Berendsen thermostat tc_grps =SYSTEM ;two coupling groups - more accurate tau_t =0.1;0.1 ;time constant, in ps ref_t =298;25 ;reference temperature, one for each \ ;group, in K ;Pressure coupling is off pcoupl =no ;no pressure coupling in NVT ;Periodic boundary conditions pbc =xyz; 3-D PBC ;Dispersion correction DispCorr=EnerPres ;account for cut-off vdW scheme ;Velocity generation gen_vel =yes;assign velocities from Maxwell distribution gen_temp=25 ;temperature for Maxwell distribution gen_seed=-1 ;generate a random seed ;END *NPT SCRIPT* File Edit Options Buffers Tools Help title =Ethanol npt equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100;save coordinates every 0.2 ps nstvout =100;save velocities every 0.2 ps nstenergy =100;save energies every 0.2 ps nstlog =100;update log file every 0.2 ps ;Bond parameters continuation=yes;Restarting after NVT constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0;short-range neighborlist cutoff (in nm) rcoulomb=1.0;short-range electrostatic cutoff (in nm) rvdw=1.0;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT
Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein
You can try Rosetta for flexible peptide docking. On 11 April 2011 15:32, Mark Abraham mark.abra...@anu.edu.au wrote: Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? I don't think anybody has the computational resources to answer this question with unguided MD. Docking programs are probably the way to get a guide about what binding modes might be reasonable, but I don't know what software might be fit for the purpose. 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/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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] g_hbond
Is it possible to find number of hydrogen bonds using g_hbond by considering the distance between Acceptor-hydrogen instead of the distance between Acceptor-Donor atoms. Nilesh On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote: Try the -contact option. Erik Nilesh Dhumal skrev 2011-04-11 17.12: Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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 -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Pressure coupling problem
Fabian Casteblanco wrote: Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for /Ethanol/ using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again looks fine. When I started running the NVT script, I set it equal to a ref_T of 298 K. It equilibrated at the temperature. Then I tried using an NPT script to equilibrate it to a ref_p of 1 bar. This is where I get the problem. The output shows the density is close to the actual experimental value of 0.789 g/cm^3. But for some reason, my pressure never gets an average of 1 bar. It keeps oscillating, which I understand is normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002). I don't understand why the ref_p of 1 bar is not working when I run this NPT.mdp script file. My simple goal is to have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1 bar and somewhere near the experimental density. Your equilibration period (100-150 ps) is rather short, and the systematic increase suggests that you're simply not equilibrated yet. Also bear in mind that a quantity that is prone to pressure fluctuations in the hundreds to thousands can only be so accurate. There was a very thorough discussion about the statistical significance of pressure values that are not equal to ref_p just some time ago. You may want to look through the archives to find this discussion. -Justin I would really appreciate anybody's help! I'm new to this but I'm eager to keep getting better. Thanks. _NVT SCRIPT (this works fine and takes me to 298 K)_ File Edit Options Buffers Tools Help title =CHARMM ETHANOL NVT equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100;save coordinates every 0.2 ps nstvout =100;save velocities every 0.2 ps nstenergy =100;save energies every 0.2 ps nstlog =100;update log file every 0.2 ps ;Bond parameters continuation=no ;first dynamics run constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0;short-range neighborlist cutoff (in nm) rcoulomb=1.0;short-range electrostatic cutoff (in nm) rvdw=1.0;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT ;Temperature coupling is on tcoupl =V-rescale ;modified Berendsen thermostat tc_grps =SYSTEM ;two coupling groups - more accurate tau_t =0.1;0.1 ;time constant, in ps ref_t =298;25 ;reference temperature, one for each \ ;group, in K ;Pressure coupling is off pcoupl =no ;no pressure coupling in NVT ;Periodic boundary conditions pbc =xyz; 3-D PBC ;Dispersion correction DispCorr=EnerPres ;account for cut-off vdW scheme ;Velocity generation gen_vel =yes;assign velocities from Maxwell distribution gen_temp=25 ;temperature for Maxwell distribution gen_seed=-1 ;generate a random seed ;END _NPT SCRIPT_ File Edit Options Buffers Tools Help title =Ethanol npt equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100;save coordinates every 0.2 ps nstvout =100;save velocities every 0.2 ps nstenergy =100;save energies every 0.2 ps nstlog =100;update log file every 0.2 ps ;Bond parameters continuation=yes;Restarting after NVT constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy
[gmx-users] Pressure coupling problem
Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for Ethanol using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again looks fine. When I started running the NVT script, I set it equal to a ref_T of 298 K. It equilibrated at the temperature. Then I tried using an NPT script to equilibrate it to a ref_p of 1 bar. This is where I get the problem. The output shows the density is close to the actual experimental value of 0.789 g/cm^3. But for some reason, my pressure never gets an average of 1 bar. It keeps oscillating, which I understand is normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002). I don't understand why the ref_p of 1 bar is not working when I run this NPT.mdp script file. My simple goal is to have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1 bar and somewhere near the experimental density. I would really appreciate anybody's help! I'm new to this but I'm eager to keep getting better. Thanks. NVT SCRIPT (this works fine and takes me to 298 K) File Edit Options Buffers Tools Help title =CHARMM ETHANOL NVT equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100 ;save coordinates every 0.2 ps nstvout =100 ;save velocities every 0.2 ps nstenergy =100 ;save energies every 0.2 ps nstlog =100 ;update log file every 0.2 ps ;Bond parameters continuation =no ;first dynamics run constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0 ;short-range neighborlist cutoff (in nm) rcoulomb =1.0 ;short-range electrostatic cutoff (in nm) rvdw =1.0 ;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME ;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT ;Temperature coupling is on tcoupl =V-rescale ;modified Berendsen thermostat tc_grps =SYSTEM ;two coupling groups - more accurate tau_t =0.1 ;0.1 ;time constant, in ps ref_t =298 ;25 ;reference temperature, one for each \ ;group, in K ;Pressure coupling is off pcoupl =no ;no pressure coupling in NVT ;Periodic boundary conditions pbc =xyz ; 3-D PBC ;Dispersion correction DispCorr =EnerPres ;account for cut-off vdW scheme ;Velocity generation gen_vel =yes ;assign velocities from Maxwell distribution gen_temp =25 ;temperature for Maxwell distribution gen_seed =-1 ;generate a random seed ;END NPT SCRIPT File Edit Options Buffers Tools Help title =Ethanol npt equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100 ;save coordinates every 0.2 ps nstvout =100 ;save velocities every 0.2 ps nstenergy =100 ;save energies every 0.2 ps nstlog =100 ;update log file every 0.2 ps ;Bond parameters continuation =yes ;Restarting after NVT constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0 ;short-range neighborlist cutoff (in nm) rcoulomb =1.0 ;short-range electrostatic cutoff (in nm) rvdw =1.0 ;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME ;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 90
-- 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 -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- Message: 4 Date: Mon, 11 Apr 2011 16:55:16 -0400 From: Fabian Casteblanco fabian.castebla...@gmail.com Subject: [gmx-users] Pressure coupling problem To: gmx-users@gromacs.org Message-ID: BANLkTikp48HDYw63W7vk8Tc=+tsjxqx...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Skipped content of type multipart/alternative-- next part -- A non-text attachment was scrubbed... Name: ethanol.itp Type: application/octet-stream Size: 2600 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110411/49df402a/ethanol.obj -- next part -- A non-text attachment was scrubbed... Name: ethanol.top Type: application/octet-stream Size: 713 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110411/49df402a/ethanol-0001.obj -- next part -- A non-text attachment was scrubbed... Name: em.gro Type: application/octet-stream Size: 449 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110411/49df402a/em.obj -- -- 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! End of gmx-users Digest, Vol 84, Issue 90 * -- 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] Pressure coupling problem
So your density graph looks stabilized? I also tend to look for changes in box x, y, z as well since the scale of their changes is easier to track. Sometimes it helps to look at the error vs. rmsd vs total drift statistics as well for such parameters that are easier to track - again if density shows stability for 0-150ps then check your boxes, it might be shrinking or growing due to the pressure perturbation, and you can use the average rate of change of those to find your equilibration point instead of trying to do something with a -300 to 300 bar pressure smear or whatnot. On 2011-04-11 04:17:59PM -0500, Justin A. Lemkul wrote: Fabian Casteblanco wrote: Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for /Ethanol/ using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again looks fine. When I started running the NVT script, I set it equal to a ref_T of 298 K. It equilibrated at the temperature. Then I tried using an NPT script to equilibrate it to a ref_p of 1 bar. This is where I get the problem. The output shows the density is close to the actual experimental value of 0.789 g/cm^3. But for some reason, my pressure never gets an average of 1 bar. It keeps oscillating, which I understand is normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002). I don't understand why the ref_p of 1 bar is not working when I run this NPT.mdp script file. My simple goal is to have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1 bar and somewhere near the experimental density. Your equilibration period (100-150 ps) is rather short, and the systematic increase suggests that you're simply not equilibrated yet. Also bear in mind that a quantity that is prone to pressure fluctuations in the hundreds to thousands can only be so accurate. There was a very thorough discussion about the statistical significance of pressure values that are not equal to ref_p just some time ago. You may want to look through the archives to find this discussion. -Justin I would really appreciate anybody's help! I'm new to this but I'm eager to keep getting better. Thanks. _NVT SCRIPT (this works fine and takes me to 298 K)_ File Edit Options Buffers Tools Help title =CHARMM ETHANOL NVT equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =5 ;2 * 5 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100;save coordinates every 0.2 ps nstvout =100;save velocities every 0.2 ps nstenergy =100;save energies every 0.2 ps nstlog =100;update log file every 0.2 ps ;Bond parameters continuation=no ;first dynamics run constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0;short-range neighborlist cutoff (in nm) rcoulomb=1.0;short-range electrostatic cutoff (in nm) rvdw=1.0;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT ;Temperature coupling is on tcoupl =V-rescale ;modified Berendsen thermostat tc_grps =SYSTEM ;two coupling groups - more accurate tau_t =0.1;0.1 ;time constant, in ps ref_t =298;25 ;reference temperature, one for each \ ;group, in K ;Pressure coupling is off pcoupl =no ;no pressure coupling in NVT ;Periodic boundary conditions pbc =xyz; 3-D PBC ;Dispersion correction DispCorr=EnerPres ;account for cut-off vdW scheme ;Velocity generation gen_vel =yes;assign velocities from Maxwell distribution gen_temp=25 ;temperature for Maxwell distribution gen_seed=-1 ;generate a random seed ;END _NPT SCRIPT_ File Edit Options Buffers Tools Help title =Ethanol npt
Re: [gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR
1. Please do not reply to the entire digest. It confuses the archive. 2. Please heed the following message from your digest: When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Miguel Quiliano Meza wrote: Dear community. Thank you for your help. After doing ./configure without problems, the system showed ERROR again after make.Here, I put the steps that I followed, what is my error?. Please help me with your advices. By the way... I made a mistake, I am using Rocks cluster 5.4. root@bioinfocluster gromacs-4.5.4]# mpi-selector-menu Current system default: openmpi-1.4-gcc-x86_64 Current user default: none u and s modifiers can be added to numeric and U commands to specify user or system-wide. 1. openmpi-1.4-gcc-i386 2. openmpi-1.4-gcc-x86_64 3. rocks-openmpi-1.4.1 4. sun-ct-8.2.1-i386 5. sun-ct-8.2.1-x86_64 U. Unset default Q. Quit Selection (1-5[us], U[us], Q): 1. export CPPFLAGS=-I/opt/rocks/include 2. export LDFLAGS=-L/opt/rocks/lib 3. 4. ./configure --enable-mpi --prefix=/share/apps/opt/gromacs * * *Until this point, I did not have errors, then...* # make The actual error message is somewhere in your ellipsis. Look at your output again and post the real error information. Also, please copy and paste your commands directly from your terminal, rather than from whatever protocol you're following. I sincerely doubt you typed 1. export CPPFLAGS... as your command. -Justin make[3]: *** [libmd.la http://libmd.la/] Error 1 make[3]: Leaving directory `/share/apps/src/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/share/apps/src/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/share/apps/src/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 *Thanks in advance. Miguel.* -- 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] g_hbond
When running g_hbond -h, I see the following, among other things: -[no]da bool yes Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) Hope that helps. Erik Nilesh Dhumal skrev 2011-04-11 23.05: Is it possible to find number of hydrogen bonds using g_hbond by considering the distance between Acceptor-hydrogen instead of the distance between Acceptor-Donor atoms. Nilesh On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote: Try the -contact option. Erik Nilesh Dhumal skrev 2011-04-11 17.12: Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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 -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] g_saltbr
Hi, I am curious how the donor and acceptor atoms are picked with g_saltbr. For examples, with Asp, it picked CG instead of the two ODs, and with LYS, it picked CE instead of NZ. Why? Thanks for your help in advance. Simon Sham -- 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] Re : Simulation for prediction of binding between a peptide and protein
but using docking I have to fix the grid and have to dock at that position... which is not my objective ... I want the peptide to come and bind own its own to the protein... I have heard of full body dock , in which there is no need to define grid points , will that be useful ?? On Mon, Apr 11, 2011 at 2:02 PM, Thomas Evangelidis teva...@gmail.comwrote: You can try Rosetta for flexible peptide docking. On 11 April 2011 15:32, Mark Abraham mark.abra...@anu.edu.au wrote: Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ?? I don't think anybody has the computational resources to answer this question with unguided MD. Docking programs are probably the way to get a guide about what binding modes might be reasonable, but I don't know what software might be fit for the purpose. 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/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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@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/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] Acpype error
Hi GMX users, When I ran acpype.py on my computer, I got one error like this: File ./acpype.py, line 67, in module from datetime import datetime ImportError: No module named datetime I use Python-2.6.6, I do not know how this error happen, could someone help me figure it out? Thanks very much in advance! -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China-- 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] g_hbond
I tried to use contact and -da together with following command g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc -noda -r 0.5 -contact -num I am getting following error. Fatal error:Can not analyze contact between H and A: turn off -noda Nilesh On Mon, April 11, 2011 5:05 pm, Nilesh Dhumal wrote: Is it possible to find number of hydrogen bonds using g_hbond by considering the distance between Acceptor-hydrogen instead of the distance between Acceptor-Donor atoms. Nilesh On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote: Try the -contact option. Erik Nilesh Dhumal skrev 2011-04-11 17.12: Is there any way to specify clorin and florin atoms as a receptor. Nilesh On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to calculate number of hydrogen bond (O-H---CL)in my system. I use the following command g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num Output file hbnum.xvg shows zero number of hydorgen bond. Can you tell me why its showing zero no. A strong peak is found in rdf between H and CL at 2.0 A. Chlorine is not considered a receptor in g_hbond. -Justin I am using Gromacs 4.0.7 version. Nilesh -- 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 -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- 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] multicomponent system- units
Hello Mark, Thank you for your reply. I have already created the energy groups. I am trying to validate pairwise energy values (nonbonded) with some other work ( a thermodynamic model) where they fit these AA AB BB (E_AA, E_AB, E_BB) energies so that some phase diagrams are reproduced. The pairwise energies defined in the model are in KJ/mol. Since my energies are not per mol, my results are useless, unfortunately. As they depend on number of molecules in the system. To achieve my goal, what do you suggest? For a binary system, can I run two separate simulations for pure A and B in which case using -nmol gives per mol energies and somehow predict AB from them? Does this make sense? Please guide me, I am stuck on this.. Thanks, On 9 April 2011 20:56, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/04/2011 12:18 PM, Elisabeth wrote: Hello everyone, I have encountered a simple problem. For a homogenous system what g_energy reports is dependent on the system size and one needs to use -nmol option to divide energies by number of molecules to obtain per mol values. I am attempting to extract interaction energies between species in a three component system. I am puzzled how this can be achieved for such a system. Say there are 100 solvent, 20 solute A and 10 B molecules. You would have to start by defining energy groups that contain relevant sets of molecules (see manual). Even once you've got them, the group-wise energies won't mean much of anything. Every observable is dependent on the configuration microstate, and unless you can estimate the relative population of different microstates to estimate a free energy... 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/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] Acpype error
Dear Qinghua Liao, Could you give a little more information about your problem? How you ran the program? ./acpype -i your_ligand_file.pdb or what? Did you tested the installation? (At folder acpype/test) Does acpype properly installed? Does Ambertools properly installed? Best regards, Aldo === Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com = --- El lun 11-abr-11, fancy2012 fancy2...@yeah.net escribió: De: fancy2012 fancy2...@yeah.net Asunto: [gmx-users] Acpype error A: gmx-users gmx-users@gromacs.org Fecha: lunes, 11 de abril de 2011, 20:27 Hi GMX users, When I ran acpype.py on my computer, I got one error like this: File ./acpype.py, line 67, in module from datetime import datetime ImportError: No module named datetime I use Python-2.6.6, I do not know how this error happen, could someone help me figure it out? Thanks very much in advance! -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China -Sigue archivo adjunto- -- 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 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
[gmx-users] orientational relaxation
dear users how can i make a orientational relaxation without traslation of molecules center of mass thanks in advances -- 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] multicomponent system- units
Hello Mark, Thank you for your reply. I have already created the energy groups. I am trying to validate pairwise energy values (nonbonded) with some other work ( a thermodynamic model) where they fit these AA AB BB (E_AA, E_AB, E_BB) energies so that some phase diagrams are reproduced. The pairwise energies defined in the model are in KJ/mol. So how did they compute these interaction energies? The energy quantity GROMACS reports for a microstate can be best thought of as the energy one would have for a mole of such microstates. Alternatively, divide by N_A and that's the energy for this microstate - but that's a much less convenient number to use. To obtain a quantity that is independent of the number of particles, you have to normalize for the number of interactions of each type. If these are all pairwise between atoms in a unary system, then you need to divide by the square of the number of atoms. So for the mixed interaction energy of the binary system, you divide by the product of the respective numbers of atoms. You should also verify that these actually are converged observables that are independent of the number of particles by simulating replicates from different starting configurations, and systems of different sizes. Mark Since my energies are not per mol, my results are useless, unfortunately. As they depend on number of molecules in the system. To achieve my goal, what do you suggest? For a binary system, can I run two separate simulations for pure A and B in which case using -nmol gives per mol energies and somehow predict AB from them? Does this make sense? Please guide me, I am stuck on this.. Thanks, On 9 April 2011 20:56, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 8/04/2011 12:18 PM, Elisabeth wrote: Hello everyone, I have encountered a simple problem. For a homogenous system what g_energy reports is dependent on the system size and one needs to use -nmol option to divide energies by number of molecules to obtain per mol values. I am attempting to extract interaction energies between species in a three component system. I am puzzled how this can be achieved for such a system. Say there are 100 solvent, 20 solute A and 10 B molecules. You would have to start by defining energy groups that contain relevant sets of molecules (see manual). Even once you've got them, the group-wise energies won't mean much of anything. Every observable is dependent on the configuration microstate, and unless you can estimate the relative population of different microstates to estimate a free energy... Mark -- gmx-users mailing list gmx-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 -- 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] orientational relaxation
dear users how can i make a orientational relaxation without traslation of molecules center of mass thanks in advances Position restraints? 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/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] Unexpected results arising from T- and P-coupling methods
Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected results (i.e. density at higher temperature is bigger than that at lower tempearature) are obtained. Generally, the latter setup is considered to be prefered to the former one in simulating realistic ensemble. I am using gmx-4.5.3, and previously I have also performed one similar work using 4.0 which can generate expected results using the latter setup. I wonder if this version 4.5.3 has some bugs in calculating T and P, and are they dealt with in 4.5.4? Please give me some hints. Yours sincerely, Chaofu Wu, Dr. -- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People’s Republic of China (P.R. China)-- 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] orientational relaxation
yes , position restraints of molecules that only allow to orient. regards. --- On Mon, 4/11/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] orientational relaxation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, April 11, 2011, 9:10 PM dear users how can i make a orientational relaxation without traslation of molecules center of mass thanks in advances Position restraints? Mark -Inline Attachment Follows- -- 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 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] orientational relaxation
yes , position restraints of molecules that only allow to orient. What's your question? Most tutorials will use position restraints at some stage. There's theory discussion in the manual. Mark regards. --- On *Mon, 4/11/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] orientational relaxation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, April 11, 2011, 9:10 PM dear users how can i make a orientational relaxation without traslation of molecules center of mass thanks in advances Position restraints? Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=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 /mc/compose?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] orientational relaxation
Hi Daniel, If you want to fix the com position, specify the molecule as comm-grps. If you really don't want movement of the com, and use pressure coupling, first put the molecule at the origin. Hope it helps, Tsjerk On Apr 12, 2011 7:28 AM, Mark Abraham mark.abra...@anu.edu.au wrote: yes , position restraints of molecules that only allow to orient. What's your question? Most tutorials will use position restraints at some stage. There's theory discussion in the manual. Mark regards. --- On Mon, 4/11/11, Mark Abraham mark.abra...@anu.edu.au wrote:From:... -- 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
