Re: [gmx-users] Simulating Multiple Solute Particles
Hi - genbox must work. You add the first molecule, then the second molecule and so on. So, I suggest to run genbox for a few times and have enough empty space available in the box. Otherwise, there is a wonderful tool called PACKMOL. The acid molecule looks pretty sexy. I guess it will not be very straighforward to capture the effect of the triple bond right near carboxyl group. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 25, 2014 at 8:23 AM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I apologize for any ignorance but I'm quite new to gromacs and am confused about a few things. I want to run some simulations of a small molecule, tetrolic acid (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a united atom approximation on the methyl group is sufficiently good for saving a bit of computation time. I have created a .gro file and a .top file and attempted to put it into gromacs but I don't know how to model more than one molecule of TTA. All of the tutorials I've looked up involve solvating enormous proteins and they only do one at a time. I'd like to simulate hundreds of TTA molecules with an appropriate amount of water molecules. I attempted to do this by specifying the numbers of TTA and H2O in my topology file, but when I tried to solvate it, gromacs removed the line specifying how many waters and replaced it with its own number (216) and made the box way too small to fit any more TTA. I feel like this may be trivial, but I'm stuck. I really appreciate anyone's help. After I figure this out, I'm going to try do dissolve tetrolic acid in chloroform, then ethanol as well. I suspect gromacs doesn't have a built in .gro or .top files for either of those (certainly not chloroform). Would the solvate command work just as well if I created my own? Thanks in advance! N.H. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot combine residue position based cog selection with index output for g_select
Hi, I'm not the expert here, but I think that gmx select -selrpos has options that you should be able to use here. See gmx help selections positions Mark On Fri, Oct 24, 2014 at 10:43 PM, Huang Dongxu fred...@gmail.com wrote: Hi, I have a system consists of a box of water and a monolayer of polymer in the center. I am trying to extract solvent molecules that have z coordinates greater than 5 nm using g_select and output an index file. Basically I want to separate my system into two portions: a box of waters above the monolayer and the rest of the system containing the monolayer. With the water only portion extracted by trajconv, I want to use genion to replace some water molecules with salt and put this modified portion back to my system that contains the monolayer. Right now, I am able to use g_select -on -select resname SOL and z5 to select all atoms that belong to SOL and has z 5 nm. However, this way does not guarantee that all the atoms selected are from SOL molecules whose cog are above z=5 plane. And as a result, some atoms that are part of SOL molecules below the z=5 plane are also selected and the entire selection contains some complete water molecules and some atoms that are from below plane water molecules (incomplete waters). I am not sure with this kind of selection, if I extract it with trajconv, and replace water with salt by genion, and then put it back to original system, will I get correct alignment of those atoms from incomplete water molecules and get the desired configuration. ( I think genion will only replace complete residue; however, when using trajconv to generate new coordination files, I am not sure if the system will be re-set to origin or not. If so then the coordinates will definitely be misplaced and when I put the modified part back there will be misalignment). TO AVOID all that, I'd like to use cog of SELECTION option in the g_select, except for 1 problems: the -on option only works with atom selection. So my essential question is: is there a way to use g_select with both the -on option and cog option? Or is there another way to finish my task? I have searched the archive and did not find something that answers my question. Thank you all for helping out. Best, Dongxu Huang Graduate student at Northwestern University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = Nose-Hoover tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = parrinello-rahman pcoupltype = Isotropic tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 refcoord-scaling = No gen-vel = no gen-temp = 298.00 gen-seed = -1 constraints = all-bonds constraint-algorithm = Lincs continuation = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for MD* integrator = md tinit = 0 dt = 0.001 nsteps = 5 ; 1 us init-step = 0 simulation-part= 1 comm-mode = Angular nstcomm = 100 comm-grps = system bd-fric = 0 ld-seed = -1 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstcalcenergy = 1 nstenergy
Re: [gmx-users] error in the middle of running mdrun_mpi
On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean there are more interactions to calculate, but the cutoffs aren't to be toyed with arbitrarily to gain speed. They are a critical element of the force field itself, though in implicit solvent, it is common to increase (and never decrease) the cutoff values used in explicit solvent. Physical validity should trump speed any day. -Justin On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = Nose-Hoover tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = parrinello-rahman pcoupltype = Isotropic tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 refcoord-scaling = No gen-vel = no gen-temp = 298.00 gen-seed = -1 constraints = all-bonds constraint-algorithm = Lincs continuation = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for MD* integrator = md tinit = 0 dt = 0.001 nsteps = 5 ; 1 us init-step =
Re: [gmx-users] error in the middle of running mdrun_mpi
regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need parallelise my simulation. I have found the same question in this mail list, one suggest use all-vs-all kernel which uses zero cut-off. This is my test run actually. I intend to run my simulation in cluster computer. On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean there are more interactions to calculate, but the cutoffs aren't to be toyed with arbitrarily to gain speed. They are a critical element of the force field itself, though in implicit solvent, it is common to increase (and never decrease) the cutoff values used in explicit solvent. Physical validity should trump speed any day. -Justin On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz
[gmx-users] histo-clust.xvg from g_clustsize
Does anyone happen to remember what the frequencies in histo-clust.xvg from g_clustsize mean? Are they directly comparable between different systems? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_distMat: A tool to calculate average min-distance matrix on multiple CPU cores
Dear GROMACS Users, I have wrote a small tool g_distMat (https://github.com/rjdkmr/g_distMat). It is almost similar to the g_mdmat. Features: Average minimum-distance matrix (residue-wise) between two index groups Related Standard deviation and variance matrix Fraction of Contacts(map) over the trajectory for residues that are within cut-off distance Parallel Calculation: uses multiple cores of CPU. Multi-threading using pthread library. With best regards, Rajendra -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to make statistics?
Hello: I am going to make statistics for how much percentage H-bond formed for residue A and B. I am just wondering how can we to do this? thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trjconv gets stuck on frame
Hello Gromacs users, I have a trajectory file script18_o.trr that I am trying to process. Using gmxcheck, this file appears to be complete. When I execute the command below trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o tmp1.trr -pbc whole EOF 0 EOF the code moves quickly through the first few hundred frames only to consistently get stuck on frame 300... trn version: GMX_trn_file (single precision) - frame320 time 128.000- frame300 time 120.000 How do I troubleshoot the problem? -Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Selecting box dimension and COM position - Pull Code
Dear Users I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am using the methodology described therein for running my own simulations. It is explained that :- GROMACS calculates distances while simultaneously taking periodicity into account. This, if you have a 10-nm box, and you pull over a distance greater than 5.0 nm, the periodic distance becomes the reference distance for the pulling, and this distance is actually less than 5.0 nm! This fact will significantly affect results, since the distance you *think* you are pulling is not what is *actually* calculated. Are there any guidelines for assigning the COM position of my biomolecule complex and the x,y,z dimensions of my simulation box keeping in mind the above explanation. Or I should go about it in a trial and error basis? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella Sampling tutorial by Dr. Justin Lemkul
Dear Users I am following the Umbrella Sampling tutorial by Dr. Lemkul and would like to have one of my doubts addressed :- After using pdb2gmx on the supplied pdb file , a topology file is obtained specifying the topology files for different protein chains in .itp format.. Inside the .itp files the inclusion of a position restraint file is also specified as follows :- ; Include Position restraint file #ifdef POSRES #include posre_Protein_chain_B.itp #endif And lastly there are .itp format position restraint files for each of the protein chains. In the tutorial it is stated that : Modify topol_Protein_chain_B.itp to include the following lines (at the end of the file): #ifdef POSRES_B #include posre_Protein_chain_B.itp #endif My question is :- Should I modify POSRES as POSRES_B or should I keep both portions by including the new lines at the end? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Time averaged ramachandran plot
Hi I plan to plot the ramachandran plot of all the dihedral angles each of which is averaged over time-frames of trajectories. But, I find g_rama or g_chi gives the time profile of ramachandran plot. But, if I want to plot the time-averaged Phi.Psi angles of all residues, is there any method to do it.ThanksSanku -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv gets stuck on frame
Hi, The output does drop in frequency at some point, so that might be all you are seeing. Experiment with -b and values around the putative problem area. Mark On Oct 26, 2014 6:59 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I have a trajectory file script18_o.trr that I am trying to process. Using gmxcheck, this file appears to be complete. When I execute the command below trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o tmp1.trr -pbc whole EOF 0 EOF the code moves quickly through the first few hundred frames only to consistently get stuck on frame 300... trn version: GMX_trn_file (single precision) - frame320 time 128.000- frame300 time 120.000 How do I troubleshoot the problem? -Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv gets stuck on frame
Hi Mark, Thank you for responding so rapidly. I should note that identical processing (I use a script) on the trajectories produced by slightly different chemical systems had no problem and trajconv produced a complete processed trajectory. However, when processing the problematic few with trajconv, the trajectory that is output is incomplete (the trjconv output has fewer frames than the input trajectory). This is definitely not problem with the change in output frequency of progress reports to the terminal. I am not sure if the -b flag is telling me anything. I move it around and it still seems to get stuck. I have ~30,000 atoms in my system. The first 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My trajectory is many nanoseconds long. Again, my other chemically similar systems do no hang like this and the simulation procedure is scripted so it is consistent across my different chemical systems. I am using gromacs/4.6.5. Best, Eric On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The output does drop in frequency at some point, so that might be all you are seeing. Experiment with -b and values around the putative problem area. Mark On Oct 26, 2014 6:59 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I have a trajectory file script18_o.trr that I am trying to process. Using gmxcheck, this file appears to be complete. When I execute the command below trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o tmp1.trr -pbc whole EOF 0 EOF the code moves quickly through the first few hundred frames only to consistently get stuck on frame 300... trn version: GMX_trn_file (single precision) - frame320 time 128.000- frame300 time 120.000 How do I troubleshoot the problem? -Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
On 10/26/14 9:55 AM, Nizar Masbukhin wrote: regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need parallelise my simulation. I have found the same question in this mail list, one suggest use all-vs-all kernel which uses zero cut-off. This is my test run actually. I intend to run my simulation in cluster computer. Unless the restriction was lifted at some point, implicit simulations won't run on more than 2 cores. There were issues with constraints that led to the limitation. -Justin On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean there are more interactions to calculate, but the cutoffs aren't to be toyed with arbitrarily to gain speed. They are a critical element of the force field itself, though in implicit solvent, it is common to increase (and never decrease) the cutoff values used in explicit solvent. Physical validity should trump speed any day. -Justin On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1
Re: [gmx-users] Selecting box dimension and COM position - Pull Code
On 10/26/14 3:43 PM, Agnivo Gosai wrote: Dear Users I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am using the methodology described therein for running my own simulations. It is explained that :- GROMACS calculates distances while simultaneously taking periodicity into account. This, if you have a 10-nm box, and you pull over a distance greater than 5.0 nm, the periodic distance becomes the reference distance for the pulling, and this distance is actually less than 5.0 nm! This fact will significantly affect results, since the distance you *think* you are pulling is not what is *actually* calculated. Are there any guidelines for assigning the COM position of my biomolecule complex and the x,y,z dimensions of my simulation box keeping in mind the above explanation. Or I should go about it in a trial and error basis? Trial and error is an awfully expensive way to determine what you need to do, when it's rather straightforward to figure out. Determine the length of the reaction coordinate you need. Based on the length of that vector in the dimensions along which the pulling takes place, it is simple to figure out the minimum size of the box in each dimension. If using pressure coupling, add a small buffer to the size to account for fluctuations. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulating Multiple Solute Particles
Thanks for your help. And actually my version of gromacs does not have genbox anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at the bottom: GENBOX - This tool has been split to gmx solvate and gmx insert-molecules.) But it's no big deal, insert-molecules seemed to work just fine! Here are the commands I used: gmx insert-molecules -f tetrolic_acid.gro -ci tetrolic_acid.gro -nmol 499 -o tetrolic500.gro gmx solvate -cp tetrolic500.gro -cs spc216.gro -o tetrolic_solv.gro -p topol.top where tetrolic_acid.gro and topol.top are files I created myself to define the molecule. I checked the output in vmd and it looks like exactly what I want. But now I'm stuck on another step and I get a confusing error. I tried to minimize the energy via: gmx grompp -f minim.mdp -c tetrolic_solv.gro -p topol.top -o em.tpr I stole the minim.mdp file from a tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp). I don't know how to properly create an mdp file from scratch, but judging from the comments, it seems reasonable and I don't see anything that must be specific to the case in the tutorial. Anyway, I don't think it caused my error. The output for that command is: Fatal error: Atomtype opls_111 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The link is not helpful, however. Googling exactly the error turns up very few results. The problem seems to be either with my topology file or with the itp file for water, which is referenced in my topology file like this: #include oplsaa.ff/tip3p.itp right after the constraints section. I also tried #include oplsaa.ff/spc.itp but it came up with a nearly identical error: Fatal error: Atomtype opls_116 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The closest thing to help I found by searching was this blog post: http://www.somewhereville.com/?p=114 However, his initial spc.itp file looks much different than mine. I think he must just have an older version of gromacs or something. Does anyone else know how I could do the energy minimization? Thanks again for all your help! N.H. - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Sent: Saturday, October 25, 2014 6:10:21 AM Subject: Re: [gmx-users] Simulating Multiple Solute Particles On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I apologize for any ignorance but I'm quite new to gromacs and am confused about a few things. I want to run some simulations of a small molecule, tetrolic acid (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a united atom approximation on the methyl group is sufficiently good for saving a bit of computation time. I have created a .gro file and a .top file and attempted to put it into gromacs but I don't know how to model more than one molecule of TTA. All of the tutorials I've looked up involve solvating enormous proteins and they only do one at a time. I'd like to simulate hundreds of TTA molecules with an appropriate amount of water molecules. I attempted to do this by specifying the numbers of TTA and H2O in my topology file, but when I tried to solvate it, gromacs removed the line specifying how many waters and replaced it with its own number (216) and made the box way too small to fit any more TTA. I feel like this may be trivial, but I'm stuck. I really appreciate anyone's help. You can adapt http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents to do this. After I figure this out, I'm going to try do dissolve tetrolic acid in chloroform, then ethanol as well. I suspect gromacs doesn't have a built in .gro or .top files for either of those (certainly not chloroform). Would the solvate command work just as well if I created my own? Yes, but perhaps gmx solvate -p won't quite do what you want. Do equilbrate that box decently; garbage in - garbage out. Mark Thanks in advance! N.H. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive
Re: [gmx-users] Simulating Multiple Solute Particles
On 10/26/14 10:49 PM, Nathan K Houtz wrote: Thanks for your help. And actually my version of gromacs does not have genbox anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at the bottom: GENBOX - This tool has been split to gmx solvate and gmx insert-molecules.) But it's no big deal, insert-molecules seemed to work just fine! Here are the commands I used: gmx insert-molecules -f tetrolic_acid.gro -ci tetrolic_acid.gro -nmol 499 -o tetrolic500.gro gmx solvate -cp tetrolic500.gro -cs spc216.gro -o tetrolic_solv.gro -p topol.top where tetrolic_acid.gro and topol.top are files I created myself to define the molecule. I checked the output in vmd and it looks like exactly what I want. But now I'm stuck on another step and I get a confusing error. I tried to minimize the energy via: gmx grompp -f minim.mdp -c tetrolic_solv.gro -p topol.top -o em.tpr I stole the minim.mdp file from a tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp). I don't know how to properly create an mdp file from scratch, but judging from the comments, it seems reasonable and I don't see anything that must be specific to the case in the tutorial. Anyway, I don't think it caused my error. The output for that command is: Fatal error: Atomtype opls_111 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The link is not helpful, however. Googling exactly the error turns up very few results. The problem seems to be either with my topology file or with the itp file for water, which is referenced in my topology file like this: #include oplsaa.ff/tip3p.itp right after the constraints section. I also tried #include oplsaa.ff/spc.itp but it came up with a nearly identical error: Fatal error: Atomtype opls_116 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The closest thing to help I found by searching was this blog post: http://www.somewhereville.com/?p=114 However, his initial spc.itp file looks much different than mine. I think he must just have an older version of gromacs or something. Does anyone else know how I could do the energy minimization? Your topology is constructed incorrectly, but without seeing it in its entirety, it is impossible to say. Please post the file for download somewhere and provide a link, otherwise copy and paste its entire contents into a reply if the message will be small enough. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to save trajectories of our interest into vmd
Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to save trajectories of our interest into vmd
Dear Suryanarayana, Try this, I hope it will help g_rmsf -f file.trr -s file.tpr -res -b 150 -e 160 -ox Required_frame.pdb On Mon, Oct 27, 2014 at 10:55 AM, Seera Suryanarayana paluso...@gmail.com wrote: Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
