[gmx-users] Freezing a portion of a protein during simulation
Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 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 = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels 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 = 300 300 ; 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 freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp
Re: [gmx-users] g_wham gets stuck
Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long and collected all the output pullf.xvg and *.tpr files. You could also run g_wham -histonly to get the histogram file. Then check with xmgrace -nxy histo.xvg whether the histograms properly overlap. But if they do not overlap, I would rather expect g_wham to give a zero PMF or to iterate forever, so not sure what is wrong. Jochen i then run g_wham (with -it and -if) and it works fine at the beginning, but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage. what is it that I'm doing wrong? it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem? this is really frustrating.. need your help, Amir -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: pull distance
Dear Gromacs Users I have set my pull option as constant force and the pull geometry is distance the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that the force applied to the protein is proportional to the distance between the 2 groups ? else what is it ? No, kJ/mol is an energy unit, so kJ/mol/nm is a force unit - the force does not depend on the distant, but is constant. One important think is that, if you want your force in pN you must transform this value to kJ/mol/nm. my second question is that what is the preferable choice for the pull ref group (pull_group0) in a protein when the force is exerted to the first and last res of the molecule . You want the first / last residue as pull_group0 / pull_group1 (or in diferent order). If you then take the full residue or only one or a couple of atoms is up to you. Greetings Thomas Best Regards Ali -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] angle
You could load your gro and trr file into vmd, label the angle, save the file and plot using excel. Oly On 28 April 2010 22:26, Justin A. Lemkul jalem...@vt.edu wrote: Nilesh Dhumal wrote: Hello, I am doing solvation of glucose. I am trying to calculate a angle between three selected carbon atoms. If I run g_angle using angle.ndx file it consider all carbon atom. In force field C-C-C 112.5 is specified so it’s making a group of all carbon atoms. I am interested in selected carbon atoms. How can I plot an angle of selected three carbon atoms? Make an appropriate index group, which it doesn't sound like you've done. If there's a specific angle you want to measure, you don't even necessarily need make_ndx, just write the group using a text editor with the appropriate atom numbers. -Justin Thanks 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] comm-grps problem gromacs 4.0.4
Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = blank and comm-grps = carb and what is below. carb is the name I use in my top file and index file. For the index I specify the groups in make_ndx and then text edit the index file and change the name to carb. I've run this simulation on a different carb before but with integrator set to md and it worked fine. Any help would be very welcome Oliver RUN CONTROL PARAMETERS integrator = sd ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= carb SOL Na ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5000 nstvout = 1 nstfout = 1 ; Checkpointing helps you continue after crashes nstcheckpoint= 5000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy= 5000 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 0 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = carb SOL Na ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 0.1 ref_t= 300 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR= no ; Relative tolerance of shake shake-tol= 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse= no -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
[gmx-users] Simulation of ONLY Lipid Bilayer
Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I need to use strong position restraints (because that is for protein and I am just using the lipid bilayer)? After the script is run, When I try doing the energy minimization, it shows unequal number of atoms in .gro and topology file. (the GRO Input has only lipid molecules where as topology files takes into account both SOL and lipid molecules). How to remove this error? I am unable to find any tutorial that could guide through the steps and the parameters to be set while doing the simulation of only bilayers. Please suggest some tutorial. Kindly guide through the steps. Regards, Saumya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulation of ONLY Lipid Bilayer
On Thu, Apr 29, 2010 at 3:29 PM, Saumya samvygu...@gmail.com wrote: Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I need to use strong position restraints (because that is for protein and I am just using the lipid bilayer)? You want to scale the lipid positions to what? InflateGro is used to pack the lipid molecules around a protein, but you want to simulate only lipids, so no point in using it. If you want to simulate a lipid bilayer, you can continue with one taken from Tieleman's site (but with what objective?). After the script is run, When I try doing the energy minimization, it shows unequal number of atoms in .gro and topology file. (the GRO Input has only lipid molecules where as topology files takes into account both SOL and lipid molecules). How to remove this error? InflateGro always removes all water (SOL) molecules. So you need to resolvate the bilayer and update your .top file accordingly. Go through the manual once. I am unable to find any tutorial that could guide through the steps and the parameters to be set while doing the simulation of only bilayers. Please suggest some tutorial. Kindly guide through the steps. Regards, Saumya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Freezing a portion of a protein during simulation
Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 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 = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels 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 = 300 300 ; 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 freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp
Re: [gmx-users] comm-grps problem gromacs 4.0.4
Oliver Grant wrote: Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = blank and comm-grps = carb and what is below. Why wouldn't your trisaccharide diffuse around? The only appropriate way to treat your system is comm-grps = System. Re-setting COM motion for different components (in a normal aqueous system) is incorrect. Membranes are a different story, but that's not important here. carb is the name I use in my top file and index file. For the index I specify the groups in make_ndx and then text edit the index file and change the name to carb. I've run this simulation on a different carb before but with integrator set to md and it worked fine. What do you mean worked fine? Your sugar didn't diffuse around? I don't see anything wrong with the behavior you've described yet. snip Tcoupl = berendsen This parameter is ignored when using the sd integrator, just FYI. ; Groups to couple separately tc-grps = carb SOL Na You should not couple ions separately from solvent: http://www.gromacs.org/Documentation/Terminology/Thermostats ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 0.1 When using sd, a small tau_t may lead to overdamping of the dynamics. I don't know specifically what implication this might have on your results, but there are a number of threads in the list archive that might give you some information. I think the general suggestion is to use tau_t = 1.0 with sd. -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Freezing a portion of a protein during simulation
Anirban Ghosh wrote: Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 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 = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels 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 = 300 300 ; 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 freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. If you're using freezegrps, I see no need to define position restraints. As for the exclusions, your group Fixed has to be listed in energygrps, and exclusions within this group are established with energygrp_excl = Fixed Fixed. There are a whole host of errors that can come up, based on what exactly Fixed comprises, but there are some good threads in the archives on how to fix these. I still think using position restraints is far easier... -Justin Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics).
[gmx-users] query about generation of 2D histogram
Respected Sir, I am trying to generate free energy landscape by using g_sham,From the archive I came to know that one .xvg file needs to be prepared containing three columns of data, first one is time, 2nd and 3rd one are the coordinates of interest, I used the command g_sham -f *.xvg -ls --histo -ngrid 40 -nlevels 30 Varying the ngrid I am getting gibbs.xpm file containing squares of different sizes. But in neither cases I am getting the histogram. I will be highly obliged if you kindly let me know how to get the histogram.I need delG values that is calculated from the equation delG=-RTln(k), where K is the joint probability of two variables.I am also eager to know how to generate the contour map from those data. reagrds Sangeeta -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] comm-grps problem gromacs 4.0.4
Thanks for the help, With center of mass removal option I thought my sugar would stay in the center of the box. It does in the first simulation I ran however what I mean by diffuse is that it leaves the box on one side and enters from the other. There is nothing physically wrong with this but I'd like the center of mass removal to keep the sugar in the center. Oliver On 29 April 2010 12:40, Justin A. Lemkul jalem...@vt.edu wrote: Oliver Grant wrote: Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = blank and comm-grps = carb and what is below. Why wouldn't your trisaccharide diffuse around? The only appropriate way to treat your system is comm-grps = System. Re-setting COM motion for different components (in a normal aqueous system) is incorrect. Membranes are a different story, but that's not important here. carb is the name I use in my top file and index file. For the index I specify the groups in make_ndx and then text edit the index file and change the name to carb. I've run this simulation on a different carb before but with integrator set to md and it worked fine. What do you mean worked fine? Your sugar didn't diffuse around? I don't see anything wrong with the behavior you've described yet. snip Tcoupl = berendsen This parameter is ignored when using the sd integrator, just FYI. ; Groups to couple separately tc-grps = carb SOL Na You should not couple ions separately from solvent: http://www.gromacs.org/Documentation/Terminology/Thermostats ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 0.1 When using sd, a small tau_t may lead to overdamping of the dynamics. I don't know specifically what implication this might have on your results, but there are a number of threads in the list archive that might give you some information. I think the general suggestion is to use tau_t = 1.0 with sd. -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 16:32 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nlmailto:x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 27 april 2010 15:37 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Interfacial systems such as membranes can translate independently of surrounding aqueous solvent. Thus, the lipids could move one way, the water can move in the other way, but overall, the net COM motion is zero. If you specify two groups, as Xavier suggested, you treat the COM motion more appropriately. So, more specifically: comm-grps = DPPC_CHOL_MOL SOL ...replacing, of course, whatever your small molecule name where I have MOL. You will need a custom index group created by make_ndx to generate this first group. -Justin Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has
Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX
Hi, (...) Output from make: = (...) /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno- unused -funroll-all-loops -L/usr/local/lib - framework Accelerate -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la - lxml2 -L/usr/X11/lib -lfftw3f -lm -lSM -lICE -lX11 cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -framework Accelerate -o grompp grompp.o -L/usr/local/lib ./.libs/libgmxpreprocess.a -L/usr/X11/lib ../mdlib/.libs/libmd.a /Users/jrui/Desktop/gromacs- 4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a /usr/lib/libxml2.dylib -lpthread -lz -licucore /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.dylib /usr/X11/lib/libICE.6.dylib /usr/X11/lib/libX11.6.dylib /usr/X11/lib/libXau.6.dylib /usr/X11/lib/libXdmcp.6.dylib ld warning: in /usr/local/lib/libfftw3f.a, file is not of required architecture What does (e.g.) nm /usr/local/lib/libfftw3f.a have to say? Also, look at ls -l /usr/local/lib/libfftw* to see whether you're picking up versions with the timestamps you expect... Maybe your FFTW configuration only installed dynamic libraries, or something. I don't know why compiling 4.0.5 would have succeeded, however. Mark Here is the output from ls: ls -l /usr/local/lib/libfftw* -rw-r--r-- 1 root wheel 2441624 Jul 21 2009 /usr/local/lib/libfftw3.a -rwxr-xr-x 1 root wheel 891 Jul 21 2009 /usr/local/lib/libfftw3.la -rw-r--r-- 1 root wheel 2370752 Jul 21 2009 /usr/local/lib/libfftw3f.a -rwxr-xr-x 1 root wheel 894 Jul 21 2009 /usr/local/lib/libfftw3f.la The output from nm /usr/local/lib/libfftw3f.a is so large that it bounced on the mailing list. Here are the first lines: nm /usr/local/lib/libfftw3f.a | head nm: no name list /usr/local/lib/libfftw3f.a(align.o): 0010 s EH_frame1 T _fftwf_alignment_of 0028 S _fftwf_alignment_of.eh /usr/local/lib/libfftw3f.a(alloc.o): 0090 s EH_frame1 0082 s LC0 008a s LC1 Also, nm -arch i386 returns: nm: file: /usr/local/lib/libfftw3f.a does not contain architecture: i386 while nm -arch x86_64 returns the same output as nm without options. Meanwhile, I went ahead and, by comparing the line where the 4.0.7 compilation fails with the corresponding line in the 4.0.5 compilation, I noticed that only difference is that the latter contains the cc extra options -m64 - std=gnu99 I guess that 64bit detection is failing. So, I passed these options to configure and the compilation went fine, producing the expected 64bit binaries: ./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib --prefix=/usr/local/gromacs407 -- program-suffix=407 CFLAGS=-m64 -std=gnu99 Thanks, Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] comm-grps problem gromacs 4.0.4
Oliver Grant wrote: Thanks for the help, With center of mass removal option I thought my sugar would stay in the center of the box. It does in the first simulation I ran however what I mean by diffuse is that it leaves the box on one side and enters from the other. There is nothing physically wrong with this but I'd like the center of mass removal to keep the sugar in the center. This is just a simple matter of periodic boundary conditions: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions You can post-process the trajectory with, i.e. trjconv -center to keep the sugar in the center of the box, but this is really only useful for visualization purposes. -Justin Oliver On 29 April 2010 12:40, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Oliver Grant wrote: Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = blank and comm-grps = carb and what is below. Why wouldn't your trisaccharide diffuse around? The only appropriate way to treat your system is comm-grps = System. Re-setting COM motion for different components (in a normal aqueous system) is incorrect. Membranes are a different story, but that's not important here. carb is the name I use in my top file and index file. For the index I specify the groups in make_ndx and then text edit the index file and change the name to carb. I've run this simulation on a different carb before but with integrator set to md and it worked fine. What do you mean worked fine? Your sugar didn't diffuse around? I don't see anything wrong with the behavior you've described yet. snip Tcoupl = berendsen This parameter is ignored when using the sd integrator, just FYI. ; Groups to couple separately tc-grps = carb SOL Na You should not couple ions separately from solvent: http://www.gromacs.org/Documentation/Terminology/Thermostats ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 0.1 When using sd, a small tau_t may lead to overdamping of the dynamics. I don't know specifically what implication this might have on your results, but there are a number of threads in the list archive that might give you some information. I think the general suggestion is to use tau_t = 1.0 with sd. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z
[gmx-users] Problem with Charmm in gromacs
Hi all, I have downloaded the latest git version of gromacs (yesterday) in which it is possible to use the charmm27 force field, I constructed the topology for my protein using the pdb2gmx program, everything goes ok also with the solvation, but then when i run the MD i notice that coulomb and LJ interaction are 0 and also the protein consequently unfold. Did any of you found this kind of problem? Could some of you rpopose eventually a solution? Thanks in advance, Fabrizio SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with Charmm in gromacs
Fabrizio Marinelli wrote: Hi all, I have downloaded the latest git version of gromacs (yesterday) in which it is possible to use the charmm27 force field, I constructed the topology for my protein using the pdb2gmx program, everything goes ok also with the solvation, but then when i run the MD i notice that coulomb and LJ interaction are 0 and also the protein consequently unfold. Did any of you found this kind of problem? Could some of you rpopose eventually a solution? Can you post your .mdp file? -Justin Thanks in advance, Fabrizio SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org ] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the
Re: [gmx-users] g_wham gets stuck
Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler. i run: *g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000*(my data is 16ns long and i ignore the first ns) and it starts reporting that the file are read: Reading file topol742.tpr, VERSION 4.0.5 (single precision) File topol742.tpr, 1 groups, geometry distance, dimensions [N Y N], (1 dimensions) grp 0) k = 1000.000 inittial distance = 2.41331 Reading file topol748.tpr, VERSION 4.0.5 (single precision) Reading file topol761.tpr, VERSION 4.0.5 (single precision) Reading file topol792.tpr, VERSION 4.0.5 (single precision) and so on.. it reports that the boundaries are found and continue to read until it stucks.. However, when i do the WHAM with the pullx files (i.e., -ix pullx-files instead of -if pullf-files.dat) the wham converges within a reasonable time to a PMF profile which not so smooth. i therefore have some questions: 1) what is the difference in the profiles for using pullx or pullf files? 2) suppose that my histograms overlap is poor for some locations along the pulling vector, how one can solve that? 3) To generate the input configurations - what is the ideal pulling procedure? ( i used pull = constant_force, with a small value of K1) Again, Thanks a lot for the quick reply Amir On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub joc...@xray.bmc.uu.se wrote: Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long and collected all the output pullf.xvg and *.tpr files. You could also run g_wham -histonly to get the histogram file. Then check with xmgrace -nxy histo.xvg whether the histograms properly overlap. But if they do not overlap, I would rather expect g_wham to give a zero PMF or to iterate forever, so not sure what is wrong. Jochen i then run g_wham (with -it and -if) and it works fine at the beginning, but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage. what is it that I'm doing wrong? it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem? this is really frustrating.. need your help, Amir -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps= DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma
Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX
- Original Message - From: J. Rui Rodrigues joaquim.rodrig...@estg.ipleiria.pt Date: Thursday, April 29, 2010 23:02 Subject: Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, (...) Output from make: = (...) /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno- unused -funroll-all-loops -L/usr/local/lib - framework Accelerate -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la - lxml2 -L/usr/X11/lib -lfftw3f -lm -lSM -lICE -lX11 cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno- unused -funroll-all-loops -framework Accelerate -o grompp grompp.o -L/usr/local/lib ./.libs/libgmxpreprocess.a -L/usr/X11/lib ../mdlib/.libs/libmd.a /Users/jrui/Desktop/gromacs- 4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a /usr/lib/libxml2.dylib -lpthread -lz -licucore /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.dylib /usr/X11/lib/libICE.6.dylib /usr/X11/lib/libX11.6.dylib /usr/X11/lib/libXau.6.dylib /usr/X11/lib/libXdmcp.6.dylib ld warning: in /usr/local/lib/libfftw3f.a, file is not of required architecture What does (e.g.) nm /usr/local/lib/libfftw3f.a have to say? Also, look at ls -l /usr/local/lib/libfftw* to see whether you're picking up versions with the timestamps you expect... Maybe your FFTW configuration only installed dynamic libraries, or something. I don't know why compiling 4.0.5 would have succeeded, however. Mark Here is the output from ls: ls -l /usr/local/lib/libfftw* -rw-r--r-- 1 root wheel 2441624 Jul 21 2009 /usr/local/lib/libfftw3.a -rwxr-xr-x 1 root wheel 891 Jul 21 2009 /usr/local/lib/libfftw3.la-rw-r--r-- 1 root wheel 2370752 Jul 21 2009 /usr/local/lib/libfftw3f.a -rwxr-xr-x 1 root wheel 894 Jul 21 2009 /usr/local/lib/libfftw3f.la The output from nm /usr/local/lib/libfftw3f.a is so large that it bounced on the mailing list. Here are the first lines: nm /usr/local/lib/libfftw3f.a | head nm: no name list /usr/local/lib/libfftw3f.a(align.o): 0010 s EH_frame1 T _fftwf_alignment_of 0028 S _fftwf_alignment_of.eh /usr/local/lib/libfftw3f.a(alloc.o): 0090 s EH_frame1 0082 s LC0 008a s LC1 Also, nm -arch i386 returns: nm: file: /usr/local/lib/libfftw3f.a does not contain architecture: i386 while nm -arch x86_64 returns the same output as nm without options. Meanwhile, I went ahead and, by comparing the line where the 4.0.7 compilation fails with the corresponding line in the 4.0.5 compilation, I noticed that only difference is that the latter contains the cc extra options -m64 - std=gnu99 I guess that 64bit detection is failing. So, I passed these options to configure and the compilation went fine, producing the expected 64bit binaries: ./configure CPPFLAGS=-I/usr/local/include LDFLAGS=- L/usr/local/lib --prefix=/usr/local/gromacs407 -- program-suffix=407 CFLAGS=-m64 -std=gnu99 It may be that the 64 bit detection is failing... comparing the output from configure in the two cases would help diagnose that. Seeing whether a fresh 4.0.5 configuration compiles might be of interest. The underlying problem might be a change in your system configuration, or the version of the autotools using in constructing 4.0.5 configure vs 4.0.7. If you really care, getting the bootstrap script from a GROMACS git distribution and running that on both your source versions should lead to both being well-formed for your system and the right flags being generated for libtool. Your work-around is probably fine, though. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The translation occurs in the z direction, yes. I'm running many constrained simulations but in general the movement of the new simulations, in which the COM translation has been removed for the bilayer and water separately, is about 1 nm in 3 ns. The movement is slower than when I was running the comm-grps = the whole system all together, but the system will still end up crossing the pbc sometime during the simulations. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r XAvier Periole [x.peri...@rug.nl] Skickat: den 29 april 2010 14:28 Till: jalem...@vt.edu; Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org ] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the bilayer should be translating in the z-dimension at all. I've done a number of simulations with this particular DPPC bilayer and never had a problem. Maybe you can also post your whole .mdp file to see if there are any problems. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my
Re: [gmx-users] Problem with Charmm in gromacs
Fabrizio Marinelli wrote: Here it is my .mdp file, i attach you also the topology file, just to be more specific the one that are 0 are the SR interactions, thank you very much. For diagnostic purposes, can you re-process your structure using a different force field and try again? If the energies are still coming up zero, then there may be something wrong in the code as a whole, otherwise it is specific to the CHARMM force field. Either way, I'm out of my league on this one :) Maybe a developer can comment. -Justin Fabrizio title= Teaa MD cpp = /lib/cpp include = integrator = md comm_mode= Linear nstcomm = 10 tinit= 0 comm-grps= System dt = 0.002 nsteps = 600 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 500 nstxtcout= 500 xtc-precision= 10 xtc_grps = System energygrps = System pbc = xyz nstlist = 5 epsilon_r= 1. ns_type = grid coulombtype = pme vdwtype = Cut-Off fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 2.2e-05 epsilon_surface = 0 optimize_fft = yes rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 tcoupl = Berendsen tc-grps = System tau_t= 1.0 ref_t= 298 pcoupl = Berendsen pcoupltype = isotropic tau_p= 2.5 compressibility = 4.5e-5 ref_p= 1.0 ; Dielectric constant of reaction field = epsilon_rf = 80.0 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint_algorithm = lincs shake_tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 user1-grps = System ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = freezedim= cos-acceleration = Fabrizio Marinelli wrote: Hi all, I have downloaded the latest git version of gromacs (yesterday) in which it is possible to use the charmm27 force field, I constructed the topology for my protein using the pdb2gmx program, everything goes ok also with the solvation, but then when i run the MD i notice that coulomb and LJ interaction are 0 and also the protein consequently unfold. Did any of you found this kind of problem? Could some of you rpopose eventually a solution? Can you post your .mdp file? -Justin Thanks in advance, Fabrizio SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the bilayer should be translating in the z-dimension at all. I've done a number of simulations with this particular DPPC bilayer and never had a problem. Maybe you can also post your whole .mdp file to see if there are any problems. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:*
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations. So if I understand correctly, you have different levels of cholesterol in DPPC, and at low cholesterol concentration you get a z-translation of your membrane, but at high concentration of cholesterol, you get no translation at all? Can you plot (using g_traj -com) the motion of the membrane to quantify just how much the membrane is moving? And again I would ask that you post your entire .mdp file, just to see your settings. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the bilayer should be translating in the z-dimension at all. I've done a number of simulations with this particular DPPC bilayer and never had a problem. Maybe you can also post your whole .mdp file to see if there are any problems. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:33 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the pbc. What type of pulling are you trying to do? Can you post your .mdp file, or at least your pull parameters? My sense is that your pull distance is greater than half the box dimension in the pull direction, causing lipids to be pulled across PBC and break down. -Justin Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 14:09 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Well 1 nm / 3 ns is definitely not reasonable! That is about 1 m / s ... 3.6 km/h We has seen motion of the COM of a bilayer using CG models but the motions were ~ 0.1 nm on the mircosecond timescale! This is due to the way COM is removed ... not exact but appears only on large time scales. On Apr 29, 2010, at 4:23 PM, ERIKSSON, EMMA wrote: The translation occurs in the z direction, yes. I'm running many constrained simulations but in general the movement of the new simulations, in which the COM translation has been removed for the bilayer and water separately, is about 1 nm in 3 ns. The movement is slower than when I was running the comm-grps = the whole system all together, but the system will still end up crossing the pbc sometime during the simulations. Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r XAvier Periole [x.peri...@rug.nl] Skickat: den 29 april 2010 14:28 Till: jalem...@vt.edu; Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial membrane configuration? -Justin ERIKSSON, EMMA wrote: Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and one with water. How is it possible that the system still is able to translate? Is there any other way to do this? Otherwise I have to manually translate the system back to its original position in the box after the simulation has crashed and then continue the simulation, but this is not very good since I cannot use the checkpoint file then and the continuation is not exact. Any suggestion what to do? Thanks in advance. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org ] för XAvier Periole [x.peri...@rug.nl mailto:x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Justin, you understood it correctly; I only have problems with the low cholesterol concentration. According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm in 3.5 ns. And as Xavier just wrote it's quite much... My mdp file looks like this: title= dppc128 cpp = /lib/cpp include = define = integrator = md dt = 0.002 nsteps = 350 ; 7 ns nstlog = 25000 nstenergy= 25 nstxout = 75 nstxtcout= 400 nstvout = 75 nstfout = 0 xtc_grps = DPPC SOL CHOL MOL energygrps = DPPC SOL CHOL MOL nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 tcoupl = Nose-hoover tc-grps = DPPC SOL CHOL MOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 323 323 323 323 Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 ref_p= 1.0 1.0 gen_vel = yes gen_temp = 323 gen_seed = 173529 constraints = all-bonds pbc = xyz optimize_fft = yes unconstrained_start = no pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.498 comm_mode= linear nstcomm = 1 comm_grps= DPPC_CHOL_MOL SOL Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:44 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations with a higher concentration of cholesterol (in which the bilayer is even more compressed and the water phase therefore is even thicker) and there is no translation in any of the simulations. So if I understand correctly, you have different levels of cholesterol in DPPC, and at low cholesterol concentration you get a z-translation of your membrane, but at high concentration of cholesterol, you get no translation at all? Can you plot (using g_traj -com) the motion of the membrane to quantify just how much the membrane is moving? And again I would ask that you post your entire .mdp file, just to see your settings. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083 comm_mode= linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL With my small molecule being MOL. I'm constraining the distance between the DPPC and the small molecule at different distances along the z direction of the bilayer. This example is for the distance being 3.083 nm between the two groups. The total z box length is ~7.2 nm. Even when I'm running without constraint the system is translating in the z direction but no crash occurs when the pbc is crossed. At this point, it would probably be useful to understand how you set up and build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is there void space in your box? Did you remove the water and re-solvate? There is no reason (in my mind) why the
[gmx-users] Hard Sphere?
Hello, I am not sure if anyone else has some experience with this, but I want to simulate a hard sphere in a solvent (water and heptane). I believe for the hard spheres, the attractive terms for LJ potential is very negligible so the only term to take into account is repulsion, from what I understand. Is there a way I can define hard sphere in gromacs? I would really appreciate some kind of direction. Thanks. -Nisha P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] unstability of system, lincs problem
Dear Justin, Thank you for your answer. Regarding the message below: 1- How is it possible to have a reasonable max force but not a resonable potential? 2- To remove this high potential from system, What do you suggest? 2-1 Do I need to reduce the number of molecules in the box (reduce density?) 2-2 Dies the idea of changinf cut off radius (you mentioned somewhere inthe archive) would work? 3- How Can I view the potential energies arising form various contributions? (electrostatics, vdw,..) to see which type is causing problem? Thank you for your help. Moeed wrote: Dear gmx experts, I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this distance!. (LINCS warning) with dt=0.002 Program mdrun, VERSION 4.0.7 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1053) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem It seems Fmax, Epot values are reasonable. . In the list archive I read I would say they are not. snip Steepest Descents converged to Fmax 1000 in 30 steps Potential Energy = 4.76092783832156e+05 Maximum force = 9.86600079729483e+02 on atom 3115 Norm of force = 5.33725886931530e+02 You have a reasonable force, but your potential energy is large and positive, indicative strong repulsive forces in your system. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these bizarre values for tau_p and compressibility in the z-dimension? I recall another post where there was an issue of z-drift like this one. You're using a tau_p in the z-dimension of 1.0x10e-14 ps - I don't even see how that's possible! It is certainly far too strenuous for P-R coupling, where you should probably be using tau_p on the order of 5-10 ps. The compressibility also doesn't make any sense to me. 4.5e-5 in all dimensions should suffice. -Justin ref_p= 1.0 1.0 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: I was using those strange values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small molecule. I was told to use those values but maybe it's not correct... I would certainly try to eliminate it as a possibility. I just don't know how the pressure coupling algorithm could possibly handle a tau_t that is several 10e-11 times smaller than the timestep! A well-equilibrated system should not fluctuate substantially over the course of a simulation, anyway. But if you need to fix the box, you *may* be able to set the relevant values of tau_t and compressibility to zero (as in the case of tau_t for temperature coupling), but I have never tried it. -Justin Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] f#246;r Justin A. Lemkul [jalem...@vt.edu] Skickat: den 29 april 2010 17:20 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these bizarre values for tau_p and compressibility in the z-dimension? I recall another post where there was an issue of z-drift like this one. You're using a tau_p in the z-dimension of 1.0x10e-14 ps - I don't even see how that's possible! It is certainly far too strenuous for P-R coupling, where you should probably be using tau_p on the order of 5-10 ps. The compressibility also doesn't make any sense to me. 4.5e-5 in all dimensions should suffice. -Justin ref_p= 1.0 1.0 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Justin A. Lemkul wrote: ERIKSSON, EMMA wrote: I was using those strange values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small molecule. I was told to use those values but maybe it's not correct... I would certainly try to eliminate it as a possibility. I just don't know how the pressure coupling algorithm could possibly handle a tau_t that is several 10e-11 times smaller than the timestep! *Edit* That should read tau_p. A well-equilibrated system should not fluctuate substantially over the course of a simulation, anyway. But if you need to fix the box, you *may* be able to set the relevant values of tau_t and compressibility to *Edit* This should also read tau_p. zero (as in the case of tau_t for temperature coupling), but I have never tried it. This one's right :) Apologies for any confusion, my brain was going faster than my fingers on this reply! -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with Charmm in gromacs
Hi Fabrizio, Could you send me the input files and I'll take a look at it. You can send it to bjelk...@cbr.su.se Regards, Pär Bjelkmar 29 apr 2010 kl. 16.34 skrev gmx-users-requ...@gromacs.org: Message: 3 Date: Thu, 29 Apr 2010 10:33:53 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Problem with Charmm in gromacs To: Gromacs Users' List gmx-users@gromacs.org Message-ID: 4bd998d1.6010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Fabrizio Marinelli wrote: Here it is my .mdp file, i attach you also the topology file, just to be more specific the one that are 0 are the SR interactions, thank you very much. For diagnostic purposes, can you re-process your structure using a different force field and try again? If the energies are still coming up zero, then there may be something wrong in the code as a whole, otherwise it is specific to the CHARMM force field. Either way, I'm out of my league on this one :) Maybe a developer can comment. -Justin Fabrizio title= Teaa MD cpp = /lib/cpp include = integrator = md comm_mode= Linear nstcomm = 10 tinit= 0 comm-grps= System dt = 0.002 nsteps = 600 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 500 nstxtcout= 500 xtc-precision= 10 xtc_grps = System energygrps = System pbc = xyz nstlist = 5 epsilon_r= 1. ns_type = grid coulombtype = pme vdwtype = Cut-Off fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 2.2e-05 epsilon_surface = 0 optimize_fft = yes rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 tcoupl = Berendsen tc-grps = System tau_t= 1.0 ref_t= 298 pcoupl = Berendsen pcoupltype = isotropic tau_p= 2.5 compressibility = 4.5e-5 ref_p= 1.0 ; Dielectric constant of reaction field = epsilon_rf = 80.0 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint_algorithm = lincs shake_tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 user1-grps = System ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = freezedim= cos-acceleration = Fabrizio Marinelli wrote: Hi all, I have downloaded the latest git version of gromacs (yesterday) in which it is possible to use the charmm27 force field, I constructed the topology for my protein using the pdb2gmx program, everything goes ok also with the solvation, but then when i run the MD i notice that coulomb and LJ interaction are 0 and also the protein consequently unfold. Did any of you found this kind of problem? Could some of you rpopose eventually a solution? Can you post your .mdp file? -Justin Thanks in advance, Fabrizio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to reduce high repulsion from system?
Dear experts, Could you please take a look at energy values. The system contains only stack of hexane molecules. MD sun gives lincs warning. 1- How can I get rid of high repulsive potential? *genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o Hexane-stack.gro* *** energy minimization my output.mdrun_em: Steepest Descents converged to Fmax 1000 in 30 steps Potential Energy = 4.76092783832156e+05 Maximum force = 9.86600079729483e+02 on atom 3115 Norm of force = 5.33725886931530e+02 * g_energy file: Statistics over 61 steps [ 0. thru 0.1200 ps ], 12 data sets All averages are exact over 61 steps Energy Average RMSD Fluct. Drift Tot-Drift -- - Angle 78416.538731.225083.3 838187 102231 LJ-141.16009e+08 8.87401e+08 8.87401e+08 3.06025e+06 373250 Coulomb-14 734.065480.683140.48113056.3 1592.44 LJ (SR) 5482.295991.074445.16 114080 13914.1 Coulomb (SR)1711.47732.288228.708 -19758 -2409.83 Potential1.16326e+08 8.8739e+08 8.8739e+08 921124 112347 Kinetic En. 1.77327e+18 5.4851e+18 4.28286e+18 9.73294e+19 1.1871e+19 Total Energy 1.77327e+18 5.4851e+18 4.28286e+18 9.73294e+19 1.1871e+19 Temperature 4.06507e+16 1.25741e+17 9.81811e+16 2.2312e+18 2.72133e+17 Pressure (bar) 1.48406e+15 4.59052e+15 3.58436e+15 8.14557e+16 9.93493e+15 T-HEX4.06507e+16 1.25741e+17 9.81811e+16 2.2312e+18 2.72133e+17 Lamb-HEX0.99144 0.00206848 0 -0.0617392 -0.00753016 Heat Capacity Cv:-0.934076 J/mol K (factor = 9.56799) *** * title = Hexane cpp = /lib/cpp ;Run control integrator = md dt = 0.002; ps ! nsteps = 5000; total 1.0 ps. nstcomm = 1; frequency for center of mass motion removal ;Output control nstenergy = 10; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 10; frequency to write coordinates/velocity/force to output trajectory file nstvout = 0 nstfout = 10 nstlog = 10; frequency to write energies to log file ;Neighbor searching nstlist = 10; neighborlist will be updated at least every 10 steps ;ns_type = grid ;Electrostatics/VdW coulombtype = cut-off vdw-type= cut-off ;Cut-offs rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ;Temperature couplingBerendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ;Pressure coupling: Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;Velocity generationGenerate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz ; ;File 'Hexane.top' was generated ;By user: moeed (500) ;On host: moeed-desktop ;At date: Thu Apr 8 13:51:19 2010 ; ;This is your include topology file ;Generated by x2top ; ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl HEX 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18 2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.3 3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.42 4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.54 5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.66 6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.84 7 opls_140 1 HEX H1 6 0.06 1.008 ; qtot -0.78 8 opls_140 1 HEX H2 6 0.06 1.008 ; qtot -0.72 9 opls_140
[gmx-users] Units + normal mode analysis
Hello, I am doing normal mode analysis for my ststem. I run the following command. g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg I could genrate the eigenfreq.xvg file. Can you tell what the units for wavenumber. It giving the unit [cm\S-1\N]. How can I convert to cm-1? Thanks 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Units + normal mode analysis
Nilesh Dhumal wrote: Hello, I am doing normal mode analysis for my ststem. I run the following command. g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg I could genrate the eigenfreq.xvg file. Can you tell what the units for wavenumber. It giving the unit [cm\S-1\N]. How can I convert to cm-1? That's exactly what it is, written in xmgrace notation (if you open it in xmgrace you'll see). \S is for superscript, \N for return to normal font. -Justin Thanks 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to reduce high repulsion from system?
Here's an excellent learning experience. 1. Simplify the problem: minimize and attempt to equilibrate one single hexane molecule before trying to build your stacked structure. If the system blows up here, then the topology is likely to blame. More on this in a few moments. 2. Watch the trajectory of the explosion, setting nstxout = 1 if necessary to catch all of the details. If you do this (with your input files below) you will see hydrogen atoms crashing in on themselves, severe angle distortions, and ultimately, collapse of the system. I would strongly suggest you do this, for your own education - knowing what to look for is half the battle. 3. Consider why this might be happening. Could x2top have given you a flawed output file? Quite possibly. Have a look at your [dihedrals] directive. Are all possible dihedrals covered? Clearly not. Every dihedral (H-C-C-H, C-C-C-C, C-C-C-H) needs to be accounted for in OPLS. You have only 5, when you should have 45 dihedral terms! Here's how I figured this out. With a molecule as simple as hexane, writing an .rtp entry is trivial, like so: [ HEX ] [ atoms ] CAA opls_157-0.180 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 HA3 opls_140 0.060 1 CAC opls_158-0.120 2 HC1 opls_140 0.060 2 HC2 opls_140 0.060 2 CAE opls_158-0.120 3 HE1 opls_140 0.060 3 HE2 opls_140 0.060 3 CAF opls_158-0.120 4 HF1 opls_140 0.060 4 HF2 opls_140 0.060 4 CAD opls_158-0.120 5 HD1 opls_140 0.060 5 HD2 opls_140 0.060 5 CAB opls_157-0.180 6 HB1 opls_140 0.060 6 HB2 opls_140 0.060 6 HB3 opls_140 0.060 6 [ bonds ] CAA HA1 CAA HA2 CAA HA3 CAA CAC CAC HC1 CAC HC2 CAC CAE CAE HE1 CAE HE2 CAE CAF CAF HF1 CAF HF2 CAF CAD CAD HD1 CAD HD2 CAD CAB CAB HB1 CAB HB2 CAB HB3 (in conjunction with the following .pdb file): HETATM1 CAA HEX 1 8.330 1.510 -0.010 1.00 20.00 C HETATM2 HA1 HEX 1 9.281 1.200 -0.024 1.00 20.00 H HETATM3 HA2 HEX 1 8.154 2.080 -0.813 1.00 20.00 H HETATM4 HA3 HEX 1 8.166 2.044 0.820 1.00 20.00 H HETATM5 CAC HEX 1 7.400 0.300 -0.030 1.00 20.00 C HETATM6 HC1 HEX 1 7.584 -0.267 0.773 1.00 20.00 H HETATM7 HC2 HEX 1 7.573 -0.231 -0.860 1.00 20.00 H HETATM8 CAE HEX 1 5.940 0.730 -0.010 1.00 20.00 C HETATM9 HE1 HEX 1 5.754 1.291 -0.816 1.00 20.00 H HETATM 10 HE2 HEX 1 5.769 1.266 0.817 1.00 20.00 H HETATM 11 CAF HEX 1 5.010 -0.480 -0.020 1.00 20.00 C HETATM 12 HF1 HEX 1 5.192 -1.038 0.790 1.00 20.00 H HETATM 13 HF2 HEX 1 5.186 -1.020 -0.843 1.00 20.00 H HETATM 14 CAD HEX 1 3.540 -0.050 -0.010 1.00 20.00 C HETATM 15 HD1 HEX 1 3.357 0.507 -0.820 1.00 20.00 H HETATM 16 HD2 HEX 1 3.363 0.489 0.813 1.00 20.00 H HETATM 17 CAB HEX 1 2.610 -1.270 -0.020 1.00 20.00 C HETATM 18 HB1 HEX 1 1.658 -0.964 -0.013 1.00 20.00 H HETATM 19 HB2 HEX 1 2.780 -1.812 -0.843 1.00 20.00 H HETATM 20 HB3 HEX 1 2.785 -1.830 0.790 1.00 20.00 H Then let pdb2gmx do the hard work for you. It will write all the necessary bonded terms, simply by specifying the bonds. Energy minimization still yields a positive potential, but it is quite low. In this case, that's alright, since there are numerous unsatisfied hydrophobic interactions that will likely be satisfied once there are a few other hexane molecules around. Equilibration works just fine after that, although I would seriously recommend *against* using cutoff electrostatics. The artefacts are well-established. Hopefully this has given you (and others who may come upon this post) some insight into how to effectively diagnose problems like this one. With more complex molecules, writing .rtp entries is not so trivial, but parameterization in general is a very advanced concept. Knowing what the force field requires is the biggest battle of all. -Justin Moeed wrote: Dear experts, Could you please take a look at energy values. The system contains only stack of hexane molecules. MD sun gives lincs warning. 1- How can I get rid of high repulsive potential? *genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o Hexane-stack.gro*
Re: [gmx-users] How to reduce high repulsion from system?
Justin A. Lemkul wrote: Here's an excellent learning experience. 1. Simplify the problem: minimize and attempt to equilibrate one single hexane molecule before trying to build your stacked structure. If the system blows up here, then the topology is likely to blame. More on this in a few moments. 2. Watch the trajectory of the explosion, setting nstxout = 1 if necessary to catch all of the details. If you do this (with your input files below) you will see hydrogen atoms crashing in on themselves, severe angle distortions, and ultimately, collapse of the system. I would strongly suggest you do this, for your own education - knowing what to look for is half the battle. 3. Consider why this might be happening. Could x2top have given you a flawed output file? Quite possibly. Have a look at your [dihedrals] directive. Are all possible dihedrals covered? Clearly not. Every dihedral (H-C-C-H, C-C-C-C, C-C-C-H) needs to be accounted for in OPLS. You have only 5, when you should have 45 dihedral terms! I should also add in here that x2top does produce the correct output if one employs the -alldih flag (which is off by default). Here's how I figured this out. With a molecule as simple as hexane, writing an .rtp entry is trivial, like so: [ HEX ] [ atoms ] CAA opls_157-0.180 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 HA3 opls_140 0.060 1 CAC opls_158-0.120 2 HC1 opls_140 0.060 2 HC2 opls_140 0.060 2 CAE opls_158-0.120 3 HE1 opls_140 0.060 3 HE2 opls_140 0.060 3 CAF opls_158-0.120 4 HF1 opls_140 0.060 4 HF2 opls_140 0.060 4 CAD opls_158-0.120 5 HD1 opls_140 0.060 5 HD2 opls_140 0.060 5 CAB opls_157-0.180 6 HB1 opls_140 0.060 6 HB2 opls_140 0.060 6 HB3 opls_140 0.060 6 [ bonds ] CAA HA1 CAA HA2 CAA HA3 CAA CAC CAC HC1 CAC HC2 CAC CAE CAE HE1 CAE HE2 CAE CAF CAF HF1 CAF HF2 CAF CAD CAD HD1 CAD HD2 CAD CAB CAB HB1 CAB HB2 CAB HB3 (in conjunction with the following .pdb file): HETATM1 CAA HEX 1 8.330 1.510 -0.010 1.00 20.00 C HETATM2 HA1 HEX 1 9.281 1.200 -0.024 1.00 20.00 H HETATM3 HA2 HEX 1 8.154 2.080 -0.813 1.00 20.00 H HETATM4 HA3 HEX 1 8.166 2.044 0.820 1.00 20.00 H HETATM5 CAC HEX 1 7.400 0.300 -0.030 1.00 20.00 C HETATM6 HC1 HEX 1 7.584 -0.267 0.773 1.00 20.00 H HETATM7 HC2 HEX 1 7.573 -0.231 -0.860 1.00 20.00 H HETATM8 CAE HEX 1 5.940 0.730 -0.010 1.00 20.00 C HETATM9 HE1 HEX 1 5.754 1.291 -0.816 1.00 20.00 H HETATM 10 HE2 HEX 1 5.769 1.266 0.817 1.00 20.00 H HETATM 11 CAF HEX 1 5.010 -0.480 -0.020 1.00 20.00 C HETATM 12 HF1 HEX 1 5.192 -1.038 0.790 1.00 20.00 H HETATM 13 HF2 HEX 1 5.186 -1.020 -0.843 1.00 20.00 H HETATM 14 CAD HEX 1 3.540 -0.050 -0.010 1.00 20.00 C HETATM 15 HD1 HEX 1 3.357 0.507 -0.820 1.00 20.00 H HETATM 16 HD2 HEX 1 3.363 0.489 0.813 1.00 20.00 H HETATM 17 CAB HEX 1 2.610 -1.270 -0.020 1.00 20.00 C HETATM 18 HB1 HEX 1 1.658 -0.964 -0.013 1.00 20.00 H HETATM 19 HB2 HEX 1 2.780 -1.812 -0.843 1.00 20.00 H HETATM 20 HB3 HEX 1 2.785 -1.830 0.790 1.00 20.00 H Then let pdb2gmx do the hard work for you. It will write all the necessary bonded terms, simply by specifying the bonds. Energy minimization still yields a positive potential, but it is quite low. In this case, that's alright, since there are numerous unsatisfied hydrophobic interactions that will likely be satisfied once there are a few other hexane molecules around. Equilibration works just fine after that, although I would seriously recommend *against* using cutoff electrostatics. The artefacts are well-established. Hopefully this has given you (and others who may come upon this post) some insight into how to effectively diagnose problems like this one. With more complex molecules, writing .rtp entries is not so trivial, but parameterization in general is a very advanced concept. Knowing what the force field requires is the biggest battle of all. -Justin Moeed wrote: Dear experts, Could you please take a look at energy values. The system contains only stack of hexane molecules. MD sun gives lincs warning. 1- How can I get rid of
