[gmx-users] Umbrella Sampling tutorial
Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix reference group to be immobile. Is it true? On the other hand, I want to know exactly using position restraining on reference group is optional or mandatory in COM pulling method? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella Sampling tutorial
Dear Justin Very thanks for your reply. What you described earlier should not be attempted with distance geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group is much more massive than the pulling group. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. You said distance geometry won't work very well in my case. What is your better suggestion about my case? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella Sampling tutorial
Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pulling force is applied. pulling direction was Z. you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12 by editconf: editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. I have a question: You said pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted.You pulled a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. Why did you used 2.4775? I think 5.0 is true. Please give me more explanation. How did you obtained this value? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella Sampling tutorial
Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1) Are these issues true about my system? lipid bilayer = reference group for pulling. drug molecule = group to which pulling force is applied. Then, should I use position restraining on the lipid bilayer? 2) The system you considered was the dissociation of a single peptide from the growing end of an protofibril. So, in your summary_distances.dat, distance between chain A and chain B was increased. But, I want to consider translocation of the drug molecule from water into the lipid bilayer. On the other hand, I want to consider approaching drug molecule to lipid bilayer. So, in my summary_distances.dat, distance between drug molecule and lipid bilayer will be decrease. My mean is that my case is contrary to your case. Nonetheless, should I use exactly Pull code section of your md_pull.mdp file? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear Justin I want to study translocation of drug molecule in lipid bilayer. My gro file after minimization is em2.gro. After NPT-MD simulation, I obtained npt.gro and 0.xtc files. When I see trajectory by vmd, there are some things abnormal. I guess there is pbc problem. I attached these 3 files. Please after viewing them, tell me is my guess true. If yes, please guide me how to fix it. If no, please tell me what is problem? https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear Justin Please check this trajectory file (1.xtc) being smaller than 0.xtc. https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear Justin I attached images related to before (em2.gro) and after equilibration. https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear Tsjerk Wassenaar Very very thanks for your reply. I used trjconv -pbc mol. pbc problem was solved only for lipid molecules. When I see new trajectory by vmd, there are some problesm about drug molecule. https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4), alternately. On the other hand, drug molecule is in region (1)in some frames and is in region (4) in other frames. Please tell me how to fix it? Is this issue (about drug molecule) pbc problem? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for lipids and not for drug molecule which is put inside water molecules in top leaflet. This pbc problem cause to drug molecule be in top and bottom leaflets, while I want to study translocation of the drug molecule from water to lipid bilayer. I want to solve this problem for drug molecule. If my manner is wrong, please tell me true way. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pbc problem
Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT 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; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; 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= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For position (a): I corrected pbc problem by trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc mol -center I selected CHOL_DOPC-drg group for centering. So problem was solved, approximately. For position (b) in which drug
[gmx-users] change of bilayer structure during NVT equilibration
Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box. I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. I did equilibration in NVT ensemble with following mdp file. -- title= NVT equilibration ; Run parameters integrator= md ; leap-frog integrator nsteps= 750 ; 2 * 750 = 15 ns dt= 0.002 ; 2 fs ; Output control nstxout= 1000 ; save coordinates every 0.2 ps nstvout= 1000 ; save velocities every 0.2 ps nstxtcout = 1000 nstenergy= 1000 ; save energies every 0.2 ps nstlog= 1000 ; 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= 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; 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= CHOL_DOPC SOL ; three coupling groups - more accurate tau_t= 0.1 0.1; time constant, in ps ref_t= 323 323; 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= 323 ; temperature for Maxwell distribution gen_seed= -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm= 5 comm-mode= Linear comm-grps= CHOL_DOPC SOL --- After 15 ns NVT equilibration, I saw obtained file (nvt.gro) by VMD. Unfortunately, rectangular shape of box was converted to cylinder shape. DOPC and CHOL molecules moved from center of box to environs of box. What is reason of this issue? Should I use new parameters in mdp file? I am beginner in gromacs. Please help me to fix this issue. Any help will highly appreciated Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] change of bilayer structure during NVT equilibration
Dear Justin Very thanks for your quick reply. Depends on how you prepared the system. For initial structure of system, I used coordination from website: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html Probably there were voids in the solvent or lipid headgroups that caused distortion in the system. When I see the initial structure of system by VMD, There is no voids in the solvent or lipid headgroups, apparently. Restraints on the lipid headgroups along z could help. I want use restraints on the dopc and chol molecules (lipid molecules). For this purpose, I did following: 1) I used genrestr tool twice. genrestr gave me 2 files (lipidchol.itp and lipiddopc.itp for cholesterol and dopc molecules, respectively). 2) I added define = -DPOSRES in mdp file. 3) I added Include Position restraint file to the topology file. My topology file is as follows: ; Include forcefield parameters #include gromos-43a1-s3_lipid.ff/forcefield.itp #include cholesterol.itp ; Include Position restraint file #ifdef POSRES #include lipidchol.itp #endif #include dopc.itp ; Include Position restraint file #ifdef POSRES #include lipiddopc.itp #endif #include gromos-43a1-s3_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif #include gromos-43a1-s3_lipid.ff/ions.itp [ system ] ; Name dopc/chol/sol [ molecules ] ; Compound#mols CHOL26 DOPC 102 SOL 1706 When I used grompp, I encountered error: Fatal error: [ file lipidchol.itp, line 34 ]: Atom index (30) in position_restraints out of bounds (1-29). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. - How to fix this issue? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Mark The UNIX tool diff is your friend for comparing files. Thanks for your suggestion. I used diff and sdiff toll for comparing 2 files (before and after correction). diff old.gro new.gro These tolls did not give me any output file or text containing difference between 2 files. In this condition, how should I find difference between 2 gro files? Best wishes for you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: - 14DOPCN4 755 0.260 1.726 6.354 14DOPCC5 756 0.263 1.741 6.204 14DOPCC1 757 0.136 1.777 6.423 14DOPCC2 758 0.279 1.580 6.384 14DOPCC3 759 0.383 1.799 6.403 14DOPCC6 760 0.386 1.685 6.132 14DOPCP8 761 0.628 1.683 6.064 14DOPC OM9 762 0.640 1.548 6.123 14DOPC OM10 763 0.747 1.771 6.072 14DOPC OS7 764 0.511 1.755 6.145 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C34 772 0.490 2.037 5.777 14DOPC OS35 773 0.541 2.029 5.644 14DOPC C36 774 0.591 2.142 5.593 14DOPC O37 775 0.595 2.252 5.646 14DOPC C38 776 0.674 2.092 5.476 14DOPC C18 777 -0.004 1.897 5.786 14DOPC C19 778 -0.138 1.837 5.744 14DOPC C20 779 -0.147 1.817 5.593 14DOPC C21 780 -0.196 1.678 5.552 14DOPC C22 781 -0.181 1.637 5.406 14DOPC C23 782 -0.252 1.722 5.301 14DOPC C24 783 -0.241 1.664 5.163 14DOPC C25 784 -0.267 1.738 5.054 14DOPC C26 785 -0.312 1.881 5.044 14DOPC C27 786 -0.368 1.918 4.907 14DOPC C28 787 -0.266 1.941 4.795 14DOPC C29 788 -0.324 2.015 4.674 14DOPC C30 789 -0.377 1.920 4.567 14DOPC C31 790 -0.377 1.984 4.428 14DOPC C32 791 -0.439 1.894 4.321 14DOPC C33 792 -0.358 1.890 4.191 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038 14DOPC C49 803 1.266 1.407 4.902 14DOPC C50 804 1.338 1.469 4.782 14DOPC C51 805 1.307 1.406 4.646 14DOPC C52 806 1.160 1.394 4.607 14DOPC C53 807 1.119 1.442 4.468 14DOPC C54 808 0.980 1.407 4.414 - after: - 14DOPCC1 755 0.136 1.777 6.423 14DOPCC2 756 0.279 1.580 6.384 14DOPCC3 757 0.383 1.799 6.403 14DOPCN4 758 0.260 1.726 6.354 14DOPCC5 759 0.263 1.741 6.204 14DOPCC6 760 0.386 1.685 6.132 14DOPC OS7 761 0.511 1.755 6.145 14DOPCP8 762 0.628 1.683 6.064 14DOPC OM9 763 0.640 1.548 6.123 14DOPC OM10 764 0.747 1.771 6.072 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C18 772 -0.004 1.897 5.786 14DOPC C19 773 -0.138 1.837 5.744 14DOPC C20 774 -0.147 1.817 5.593 14DOPC C21 775 -0.196 1.678 5.552 14DOPC C22 776 -0.181 1.637 5.406 14DOPC C23 777 -0.252 1.722 5.301 14DOPC C24 778 -0.241 1.664 5.163 14DOPC C25 779 -0.267 1.738 5.054 14DOPC C26 780 -0.312 1.881 5.044 14DOPC C27 781 -0.368 1.918 4.907 14DOPC C28 782 -0.266 1.941 4.795 14DOPC C29 783 -0.324 2.015 4.674 14DOPC C30 784 -0.377 1.920 4.567 14DOPC C31 785 -0.377 1.984 4.428 14DOPC C32 786 -0.439 1.894 4.321 14DOPC C33 787 -0.358 1.890 4.191 14DOPC C34 788 0.490 2.037 5.777 14DOPC OS35 789 0.541 2.029 5.644 14DOPC C36 790 0.591 2.142 5.593 14DOPC O37 791 0.595 2.252 5.646 14DOPC C38 792 0.674 2.092 5.476 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038
[gmx-users] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your consideration. I ignored Warning 1. WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Based on your suggestion, I checked non-matching atom names between topol.top and system.gro files. I corrected system.gro file accordance with topol.top file. I did this work very carefully. I was watchful to not disturb the format of the system.gro file, so that when I saw system gro file (before and after the correction) by an editor program, both of them were same. But, when I use grompp, I encountered with: Fatal error: Something is wrong in the coordinate formatting of file sys.gro. Note that gro is fixed format (see the manual). How to solve this problem? Any help will highly appreciated. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your consideration. My system contains 2 components: (DOPC cholesterol) lipids + water molecules. I get force field parameters from lipid book (for dopc and cholesterol). I used input coordinate file (system.gro) from following web site: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html em.mdp file is as follows: - ; em.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions - For doing minimization, I used following command: grompp -f em.mdp -c system.gro -p topol.top -o em.tpr and then I get following result: - WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Analysing residue names: Warning: file does not end with a newline, last line: IB+ Ion There are: 128 Other residues There are: 1706 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 29019.00 Largest charge group radii for Van der Waals: 1.541, 1.514 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (3.054313) is larger than rlist (1.20) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 133 Mb of data There was 1 note There were 2 warnings - I used -maxwarn option and I obtained em.tpr file. Then, for doing minimization, I used following command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log and then I get following result: - Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 - When I see created gro file (em.gro) by VMD, some dopc or cholesterol molecules are broken to 2 or 3 parts. I tested different ways: 1) change of parameters in em.mdp file ( emstep, nstep, EM algorithm ) 2) change of box size 3) I used the newest version of gromacs (4.6.3) But, unfortunatele, my problem was not solved. Certainly, I can not use this structure for next step (equilibration). How to solve this problem. Any help will highly appreciated. Best wishes for you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
[gmx-users] Re: grompp for minimization: note warning
Dear Justin I used newer version of gromacs (4.6.1), but my problem was not solved. Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Thanks for your reply You're still working with outdated software. Please follow my suggestion of trying 4.6.3. I try to install 4.6.3. The larger issue, in the end, is the unphysical configuration of the drug in the membrane. Independent of Gromacs version, that setup will always fail. I did minimization in 2 other states: 1) without drug (only membrane: DOPC nad cholesterol). 2) with drug but, this time, I put drug into water molecules not into membrane. Then I did mdrun for both of states. In both of state, there are not following issues: Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates -- There are following outputs: for state 1) - Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 for state 2) Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 845 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.9664772e+05 Maximum force = 1.0986521e+04 on atom 241 Norm of force = 4.4174323e+02 --- When I see created gro file from minimization (em.gro), I see some dopc and cholesterol molecules were broken and they devided 2 or 3 parts. Input gro file (system.gro) has 1835 residues. Created gro file from minimization (em.gro) has 1835 residues. But when I load em.gro file in VMD, there are 1950 residues in graphical representation -- selections -- residues part. Can I deduce my problem has not dependent to presence of drug? Are there problem about my force field parameters or topology file ? I get force field parameters from lipid book (for dopc and cholesterol) and from prodrg server (for drug). Please help me to resolve this issue. Best wishes for you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Thanks for your time and consideration. As I suggested before, visualize the output file and figure out what is around atom 618 to cause such forces. I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc molecule (this dopc molecule is intact and is not broken). There are other dopc and cholesterol molecules around atom 618. How I understand what around this atom cause such forces. Excuse me. Please give me more explanation about your suggestion. May be, I did not understand your mean truly. Should I remove this dopc molecule and then run minimization again? PRODRG generates notoriously bad parameters, particularly the charges. I know this issue, charges and charges groups obtained from prodrg (in itp file) were compared with charges and charges groups in similar structures being in rtp file of gromos (because my drug is very similar to cytosine). Then I corrected them. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. I am very confused and amazed. After visualization of atom 618 ( where the maximum force is), what should I do to resolve me problem. Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp for minimization: note warning
Dear Justin I did minimization with the newest version of gromacs (4.6.3). But, unfortunately, problem was not solved. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp for minimization: note warning
Dear Justin Very thanks for your reply. You said I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check. I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. Based on your suggestion, I used -maxwarn option for grompp. Then I used -nt 1 option for mdrun, but this step takes too long and Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2122 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.4310875e+05 Maximum force = 2.7179752e+04 on atom 5271 Norm of force = 4.0253470e+02 -- my em.mdp file is as follows: integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions -- gro, edr, trr and lof file were created. I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp file, but result are the same. Is this minimization completely true? Can I use created gro file of this minimization for next step (equilibration)? I am beginner in gromacs, please help me to resolve this problem. Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp for minimization: note warning
Dear Justin About following warning in grompp using WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) You said You probably have molecules split across PBC in the input coordinate file. here's nothing wrong in that case I mention that I used input coordinate file from folloowing web site http://cmb.bio.uni-goettingen.de/cholmembranes.html. Structures in this website were equilibrated 195 ns. Nonetheless, has my input coordinate file problem? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. Please guide me to resolve these issues. Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. Please guide me to resolve these issues. Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp for minimization: note warning
Dear gromacs users My system contains 3 components: DOPC cholesterol lipids + drug + water molecules. In minimization step, when I use grompp -f em.mdp -c system.gro -p topol.top -o em.tpr, I encountered with following note and warning: WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing --- My em.mdp file is as follows: ; em.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions - I dont like to use -maxwarn option. How to modify parameters in em.mdp file to resolve note an warning. Any help will highly appreciated. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp for minimization: note warning
Dear gromacs users Nember of groups in each of charge groups is less than or equal 3. charge groups in my itp files are as follows: DOPC.itp: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CH3* 1 DOPC C1 10.4 15.035 2 CH3* 1 DOPC C2 20.4 15.035 3 CH3* 1 DOPC C3 30.4 15.035 4NL 1 DOPC N4 4 -0.514.0067 5 CH2* 1 DOPC C5 50.3 14.027 6 CH2* 1 DOPC C6 60.4 14.027 7OA 1 DOPCOS7 7 -0.815.9994 8 P 1 DOPC P8 81.730.9738 9OM* 1 DOPCOM9 9 -0.815.9994 10OM* 1 DOPC OM10 10 -0.815.9994 11OA 1 DOPC OS11 11 -0.715.9994 12CH2* 1 DOPCC12 120.4 14.027 13 CH1* 1 DOPCC13 130.3 13.019 14OA 1 DOPC OS14 14 -0.715.9994 15CO* 1 DOPCC15 150.7 12.011 16 O* 1 DOPCO16 16 -0.715.9994 17 CH2* 1 DOPCC17 17 0 14.027 18 CH2* 1 DOPCC18 17 0 14.027 19 CH2* 1 DOPCC19 17 0 14.027 20 CH2* 1 DOPCC20 18 0 14.027 21 CH2* 1 DOPCC21 18 0 14.027 22 CH2* 1 DOPCC22 18 0 14.027 23 CH2* 1 DOPCC23 19 0 14.027 24 C*H1 1 DOPCC24 19 0 13.019 25 C*H1 1 DOPCC25 19 0 13.019 26 CH2* 1 DOPCC26 20 0 14.027 27 CH2* 1 DOPCC27 20 0 14.027 28 CH2* 1 DOPCC28 20 0 14.027 29 CH2* 1 DOPCC29 21 0 14.027 30 CH2* 1 DOPCC30 21 0 14.027 31 CH2* 1 DOPCC31 21 0 15.035 32 CH2* 1 DOPCC32 22 0 14.027 33 CH3* 1 DOPCC33 220.0 15.035 34 CH2* 1 DOPCC34 230.5 14.027 35OA 1 DOPC OS35 24 -0.715.9994 36CO* 1 DOPCC36 250.8 12.011 37 O* 1 DOPCO37 26 -0.615.9994 38 CH2* 1 DOPCC38 27 0 14.027 39 CH2* 1 DOPCC39 27 0 14.027 40 CH2* 1 DOPCC40 27 0 14.027 41 CH2* 1 DOPCC41 28 0 14.027 42 CH2* 1 DOPCC42 28 0 14.027 43 CH2* 1 DOPCC43 28 0 14.027 44 CH2* 1 DOPCC44 29 0 14.027 45 C*H1 1 DOPCC45 29 0 13.019 46 C*H1 1 DOPCC46 29 0 13.019 47 CH2* 1 DOPCC47 30 0 14.027 48 CH2* 1 DOPCC48 30 0 14.027 49 CH2* 1 DOPCC49 30 0 14.027 50 CH2* 1 DOPCC50 31 0 14.027 51 CH2* 1 DOPCC51 31 0 14.027 52 CH2* 1 DOPCC52 31 0 14.027 53 CH2* 1 DOPCC53 32 0 14.027 54 CH3* 1 DOPCC54 32 0 15.035 cholesterol.itp: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1CH2R61CHOL C110.014.027 2CH2R6 1 CHOLC220.0 14.027 3CH1R6 1 CHOLC330.270 13.019 4CH2R6 1 CHOLC440.0 14.027 5C* 1 CHOLC550.012.011 6C*HR6 1 CHOLC660.0 13.019 7CH2R6 1 CHOLC770.0 14.027 8CH1R61 CHOLC880.013.019 9CH1R6 1 CHOLC990.0 13.019 10CH0*1 CHOLC10100.012.011 11CH2R6 1 CHOLC11110.0 14.027 12CH2R6 1 CHOLC12120.0 14.027 13CH0*1 CHOLC13130.0 12.011 14 CH1R6 1 CHOLC14 14 0.0 13.019 15CH2R51 CHOLC15150.0 14.027 16CH2R5 1 CHOLC16160.0 14.027 17 CH1R5 1
[gmx-users] grompp for minimization: note warning
Dear gromacs users I used -maxwarn option, but after using this command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log I encountered with: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 6.61528 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Based on above suggestion, I should use option -rdd with mdrun, but I dont what argument with -rdd? What value is appropriate for -rdd? 0 or other? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromos force field in PRODRG server
Dear gromacs users I want to do MD simualation for a protein-ligand system. For ligand, I use PRODRG server. I know that this server generate a *.itp file for ligand based on gromos force field. There are 5 versions for gromos force field (GROMOS96 43a1, GROMOS96 43a2, GROMOS96 45a3, GROMOS96 53a5, GROMOS96 53a6) in gromacs package. what version of mentioned versions of gromos force field is used in PRODRG server to generate a *.itp file for ligand? In fact, I want to know what version of gromos force fields I should use for protein. Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] difference between restrained and constrained
Dear gromacs users I want to know what is difference between restrained EM and restrained EM or between constrained MD and constrained MD. any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] radius of gyration - compactness - accessible surface area
Dear Tsjerk very thanks for your useful guidance. I now know that I should compare output of g_gyrate (containing Rg vs time) by area.xvg output file of g_sas (containing area vs time). In area.xvg output file, there are several columns: Hydrophobic, Hydrophilic and Total. for example in time, 100 ps: 10035.9501 60.9389 96.8891 area is in nm2. from above number I understand that 35.9501 nm2 of area of protein that is accessible to solvent belongs to hydrophobic part of protein. and 60.9389 nm2 of area of protein that is accessible to solvent belongs to hydrophilic part of protein. is my understanding true? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] radius of gyration - compactness
Dear all I am studying md simulation of free protein and protein-ligand and protein-dna complex. In my simulation systems, the average of radius of gyration in free protein is 2.31 and for protein in complex is 2.58. I know the radius of gyration is measurement of compactness of the protein as smaller radius of gyration indicates protein is more compact,. I encountered antithesis in two following paper: 1- The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis. J. Mol. Recognit. 2004; 17: 120–131. [ Furthermore, INT–DBD appears less compact in the complex, as far as the radius of gyration increases and more molecular surface is exposed to the solvent (Table 1). ] 2- Molecular dynamics analysis of the engrailed homeodomain–DNA recognition. Journal of Structural Biology 155 (2006) 426–437. [ Furthermore, according to radiuses of gyration of two proteins in the two systems, the protein in the complex is more compact than the free protein, this is consistent with the result of structure stability comparing. It means that less molecular surface of homeodomain protein in the protein– DNA complex is exposed to the solvent.] please guide me about that. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] adius of gyration - compactness
Dear Tsjerk thanks for your reply. in paper 1 : larger radius of gyration, less compact, more surface in paper 2: (smaller radius of gyration; not stated explicitly), more compact, less surface. in paper 3: [Journal of Structural Biology 156 (2006) 537–545] Overall, the GBD appears a little more compact in the complex, as far as the radius of gyration decrease and less molecular surface is exposed to the solvent. all of above is true. I want to know exactly how do radius of gyration of protein from free state to complex state change . Rg increased od decreased? What's the contradiction? contradiction is in this that in paper 1 Rg increased and in paper 2 and 3 decreased. I want to know my data [ In my simulation systems, the average of radius of gyration in free protein is 2.31 and for protein in complex is 2.58.] is true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] radius of gyration - compactness - accessible surface area
Dear Tsjerk thanks for your attention. larger radius of gyration, more surface. and smaller radius of gyration, less surface. I want to obtain solvent accessible surface area using g_sas. g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa. I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg If I want to obtain average of ASA to compare with Rg (I want to know in my system, with increase of Rg, how do ASA change?), which of above output files are suitable for this aim? best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] radius of gyration - compactness - accessible surface area
Dear Tsjerk thanks for your attention. larger radius of gyration, more surface. and smaller radius of gyration, less surface. I want to obtain solvent accessible surface area using g_sas. g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa. I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg If I want to obtain average of ASA to compare with Rg (I want to know in my system, with increase of Rg, how do ASA change?), which of above output files are suitable for this aim? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] standard deviation about rmsd and rmsf values
Dear gromacs users I want to know how to obtain standard deviation about rmsd and rmsf values? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to obtain binding energy?
Dear Justin thanks for your time and attention in address http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html in Tutorial 3: Umbrella Samplinghttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html, in Step One, you said '' For protein-ligand systems, please consult this tutorial http://eugen.leitl.org/chem/kerrigje/pdf_files/trp_drug_tutor.pdf'' . unfortunately, I can't access that (when clicked on link: Apologies, but the page you requested could not be found). how to access to that link? I have another question about my system (protein-dna complex). If I do a mutation in protein, can I obtain delta delta G by PMF method again? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to obtain binding energy
Dear gromacs users my simulation system is protein-ligand. I did 3 simulations. protein only, ligand only and protein-ligand complex. I want to know how to obtain binding energy between protein and ligand by MD simulation using gromacs. any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to obtain binding energy?
Dear mohsen thanks for your reply. I forgot to say there are water and ion in my system. with new conditions, can I use PMF or TI? I have another question: is there this possibility to obtain affinity between protein and ligand by gromacs? please guide me about that. best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to obtain binding energy?
Dear Justin thanks for your attention *Do you mean binding constants? * yes, I mean Ka or Kd. what about protein-dna complex? can I use PMF or TI for that to obtain binding free energy? best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to obtain binding energy?
Dear Justin and Mohsen Very thanks for your attention Justin you said PMF is much easier in my case (protein-dna complex). Is there tutorial or example about using PMF method in gromacs to obtain free binding energy? If so, please address me. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond -ac -life
Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? any help will highly appreciated -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond -ac -life
Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] hblife.xvg and hbac.xvg files
Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] difference between p(t) and c(t)
Dear all I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] hblife.xvg and hbac.xvg files
Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond / hbmap.xpm file
Dear Erik Thanks for your attention. What is your mean of [but keep in mind that the matrix is displayed with the first row at the bottom]. Please clarify that more. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond / hbmap.xpm file
Dear gromacs users I used g_hbond -f *.xtc -s *.tpr -n *.ndx -hbm hbmap.xpm for hydrogen bond analysis. then I used xpm2ps -f hbmap.xpm -o hbmap.eps.the ps file is hydrogen bond index vs time. I don't understand numbers in vertical axis. do these numbers in vertical axis relate to hbond.ndx file? how? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond / hbmap.xpm file
Dear Erik and Justin
Thanks for your time and attention.
My xpm file is following state:
/* XPM
*/
/* Generated by g_hbond
*/
/* This file can be converted to EPS by the GROMACS program xpm2ps
*/
/* title: Hydrogen Bond Existence Map
*/
/* legend: Hydrogen Bonds
*/
/* x-label: Time (ps)
*/
/* y-label: Hydrogen Bond Index
*/
/* type:Discrete
*/
static char *gromacs_xpm[] =
{
126 40 4
1,
c #FF /* None
*/,
o c #FF /* Present
*/,
- c #FF /* Inserted
*/,
* c #FF00FF /* Present Inserted
*/,
/* x-axis: 19500 19504 19508 19512 19516 19520 19524 19528 19532 19536
19540 19544 19548 19552 19556 19560 19564 19568
/* y-axis: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 0 */
o
o ,
ooo ooo o o
o o oo,
ooo ooo oo
ooo oo oo,
oo oo ooo ooo ooo ooo ooo oo ooo oo
o o o o oo o oo oo oo oo o,
o
o ,
oo o oo oo ooo
o,
oo oo ooo o oo oo o ooo
ooo oo o oo ooo o o oo ooo ,
o oo o o o,
o o oo
o o oo o o ,
o
o ,
oo,
o o o
o o ,
o o ooo ooo o oo
oo o oo o oo o o o,
and h-bond section of .ndx file is as follows:
[ hbonds_Protein -Ligand ]
1019 1021 1640
1019 1021 1643
1019 1021 1656
1013 1014 1643
995997 1580
992994 1580
992994 1581
992994 1582
946949 1135
915917 1580
915917 1581
909910 1580
909910 1581
867869 1212
777780 1517
777780 1518
740742 1198
723725 1231
720722 1231
504506 1516
504506 1517
501503 1516
103104 1166
103104 1168
95 97 1198
92 93 1174
92 93 1196
79 80 1166
79 80 1168
63 64 1835
32 33 1752
26 29 1784
26 29 1787
1791 1793 45
1755 1757 9
1627 1629852
1627 1629853
1597 1599852
1215 1217866
1215 1217867
what is your mean of reading backward .xpm? above files or ps file obtained
from xpm2ps.
--
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[gmx-users] g_hbond / hbmap.xpm file
Dear Justin Thus, if there are 40 hydrogen bond. Numerical indice 5 on the y-axis of .eps file is same to indice 35 in .ndx file. Is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond / lifetime
Dear all I used g_hbond for analysis of hydrogen bonds between protein-ligand complex. g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist after using g_hbond, gromacs gives me: HB lifetime = 16.82 ps this lifetime is related with what hydrogen bond? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond / lifetime
Dear Dallas Warren Thanks for your attention. Thus, if I select a certain hydrogen bond from *.ndx file, g_hbond give me HB lifetime only for that certain hydrogen bond. Is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv -pbc/ box/ solvent
Hi gromacs users I want to know after using trjconv -pbc, box disappears and solvent molecule recedes from solute. is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv -pbc/box /solvent
Dear Justin thanks for your attentions In my case, after md simulation my protein diffuse out from one side of box. for solution I used trjconv -pbc nojump. then problem fixed but box disappears and water molecules recedes from protein. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] yes/no
Hi gromacs users In gromacs manual, in appendix section, for every tool, in Files section, there are input and output files needed for analysis. but in Other options section, there are some things that I don't understand. Is third column of Other opthions default values? In third column of Other opthions, somewhen, yes or no is seen. What does yes mean? What does no mean? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] yes/no
Hi Justin thanks for your attention. in editconf instance, if I don't use -c, this is same mean with -noc? In third column of Other opthions, somewhen, 1 and -1 is seen. What does 1 mean? What does -1 mean? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] yes/no
Dear Justin I understood. for instance, in trjconv -dump (-1), What does it mean? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] yes/no
Dear Justin thanks thus, if I want to set 800 ps for -dump, -dump 796 is true (every frame is 4 ps). ok? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] -pbc nojump
Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gibbs free energy of binding
Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] -tu flag in g_hbond
Hi gromacs users in g_hbond command there is not -tu flag and I want to have time unit as ns no default form (ps). What is the best way to do this? Please suggest. -- 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] -tu flag in g_hbond
Dear Justin thanks for your attention. this file that I want to be as ns is hbmap.xpm I did following steps to obtain pdf file : 1) xpm2ps 2) ps2pdf can I open xpm file by xmgrace? -- 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] -tu flag in g_hbond
Dear Justin I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: Hydrogen Bond Existence Map */ /* legend: Hydrogen Bonds */ /* x-label: Time (ns) */ /* y-label: Hydrogen Bond Index */ /* type:Discrete */ I changed x-label: Time (ps) to x-label: Time (ns) . but only label of x-axis was changed. please guide me -- 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] -tu flag in g_hbond
Dear Justin *excuseme this email is true.* I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: Hydrogen Bond Existence Map */ /* legend: Hydrogen Bonds */ /* x-label: Time (ps) */ /* y-label: Hydrogen Bond Index */ /* type:Discrete */ I changed x-label: Time (ps) to x-label: Time (ns) . but only label of x-axis was changed. please guide me -- 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] g_rama / mult
Hi all I used [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of protein. gromacs give me rama.xvg as output but during calculation : Found 68 phi-psi combinations Dihedral around 9,11 not found in topology. Using mult=3 Dihedral around 11,18 not found in topology. Using mult=3 Dihedral around 20,22 not found in topology. Using mult=3 Dihedral around 22,29 not found in topology. Using mult=3 Dihedral around 33,36 not found in topology. Using mult=3 Dihedral around 40,47 not found in topology. Using mult=3 Dihedral around 51,58 not found in topology. Using mult=3 Dihedral around 62,65 not found in topology. Using mult=3 Dihedral around 301,303 not found in topology. Using mult=3 Dihedral around 303,314 not found in topology. Using mult=3 Dihedral around 318,336 not found in topology. Using mult=3 Dihedral around 340,358 not found in topology. Using mult=3 Dihedral around 360,362 not found in topology. Using mult=3 Dihedral around 362,378 not found in topology. Using mult=3 Dihedral around 382,393 not found in topology. Using mult=3 Dihedral around 397,407 not found in topology. Using mult=3 Dihedral around 411,424 not found in topology. Using mult=3 Dihedral around 428,446 not found in topology. Using mult=3 Dihedral around 450,467 not found in topology. Using mult=3 Dihedral around 471,486 not found in topology. Using mult=3 Dihedral around 490,497 not found in topology. Using mult=3 Dihedral around 509,511 not found in topology. Using mult=3 Dihedral around 523,525 not found in topology. Using mult=3 Dihedral around 529,540 not found in topology. Using mult=3 Dihedral around 544,564 not found in topology. Using mult=3 Dihedral around 568,586 not found in topology. Using mult=3 Dihedral around 590,610 not found in topology. Using mult=3 Dihedral around 614,629 not found in topology. Using mult=3 Dihedral around 633,639 not found in topology. Using mult=3 Dihedral around 643,661 not found in topology. Using mult=3 Dihedral around 665,678 not found in topology. Using mult=3 Dihedral around 682,697 not found in topology. Using mult=3 Dihedral around 701,714 not found in topology. Using mult=3 Dihedral around 718,733 not found in topology. Using mult=3 Dihedral around 737,744 not found in topology. Using mult=3 Dihedral around 748,759 not found in topology. Using mult=3 Dihedral around 763,783 not found in topology. Using mult=3 Dihedral around 787,800 not found in topology. Using mult=3 Dihedral around 804,816 not found in topology. Using mult=3 Dihedral around 820,838 not found in topology. Using mult=3 Dihedral around 842,852 not found in topology. Using mult=3 Dihedral around 856,876 not found in topology. Using mult=3 Dihedral around 880,896 not found in topology. Using mult=3 Dihedral around 900,913 not found in topology. Using mult=3 Dihedral around 917,927 not found in topology. Using mult=3 Dihedral around 931,951 not found in topology. Using mult=3 Dihedral around 955,975 not found in topology. Using mult=3 Dihedral around 979,985 not found in topology. Using mult=3 Dihedral around 989,1007 not found in topology. Using mult=3 Dihedral around 1011,1031 not found in topology. Using mult=3 Dihedral around 1035,1055 not found in topology. Using mult=3 Dihedral around 1059,1079 not found in topology. Using mult=3 Dihedral around 1083,1090 not found in topology. Using mult=3 Dihedral around 1094,1097 not found in topology. Using mult=3 Dihedral around 1109, not found in topology. Using mult=3 Dihedral around 1115,1122 not found in topology. Using mult=3 Dihedral around 1126,1133 not found in topology. Using mult=3 is this rama.xvg file true and intact? -- 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] g_rama / mult
Dear Tsjerk Wassenaar thanks for your attentions. ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] is my actual command line. I get tpr file by command : grompp -f *.mdp -c *.gro -p *.top -n *.ndx -o *.tpr where I should put multiplicity of 3 (what file) ? -- shahab -- 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] B-factor
Hi all excuse me for my past incomplete email. I want to calculate B-factor using g_rmsf command as follows: g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq this command give me a pdb file whereas I want to obtain text file (numeral value of B-factor ). how to obtain B-factor value from this pdb file? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] B-factor
Hi all I want to calculate B-factor using g_rmsf command as follows g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq -- 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] B-factor
Dear *Erik Marklund* what do you meant from See the reference for the pdb file format? is b-factor a file? please guide me more. I am beginner in gromacs. -- 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] B-factor
Dear Erik Marklund thanks for your attention I saw www.pdb.org. there is b-factor in pdb files being in this website but pdb file obtained form g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command, has not B-factor. my bfac.pdb file is as follows : TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 62.008 62.008 62.008 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00272.65 ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 ATOM 23 CA SER 3 25.254 48.487 33.290 1.00189.09 ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00114.27 ATOM 41 CA SER 5 27.814 48.657 27.860 1.00195.51 ATOM 52 CA SER 6 31.164 48.167 26.020 1.00217.99 ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00300.70 ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00248.64 ATOM 92 CA GLY 9 35.314 45.957 18.630 1.00184.40 ATOM 99 CA GLY 10 37.064 42.607 19.150 1.00139.99 ATOM 106 CA GLN 11 37.224 39.007 17.810 1.00106.39 ATOM 123 CA VAL 12 34.754 36.657 19.540 1.00 78.29 ATOM 139 CA ARG 13 33.244 33.847 17.550 1.00 79.41 ATOM 163 CA PHE 14 32.044 30.277 17.980 1.00 23.96 ATOM 183 CA SER 15 30.254 27.737 15.740 1.00 44.68 ATOM 194 CA ASN 16 26.794 26.277 16.430 1.00 54.17 ATOM 208 CA ASP 17 28.154 23.097 18.090 1.00 52.38 ATOM 220 CA GLN 18 30.914 24.937 19.880 1.00 25.27 ATOM 237 CA THR 19 28.404 27.377 21.340 1.00 24.72 ATOM 251 CA ILE 20 26.264 24.487 22.620 1.00 35.92 ATOM 270 CA GLU 21 29.004 22.497 24.430 1.00 22.96 ATOM 285 CA LEU 22 30.324 25.797 25.950 1.00 13.17 ATOM 304 CA GLU 23 26.874 26.467 27.560 1.00 26.01 ATOM 319 CA LYP 24 26.474 22.877 28.710 1.00 37.38 ATOM 341 CA LYP 25 29.944 22.657 30.270 1.00 29.72 ATOM 363 CA PHE 26 29.484 26.037 32.040 1.00 33.01 ATOM 383 CA GLU 27 26.304 24.837 33.730 1.00 56.55 ATOM 398 CA THR 28 28.194 21.907 35.400 1.00 71.22 ATOM 412 CA GLN 29 31.264 24.057 36.290 1.00 61.11 ATOM 429 CA LYP 30 31.314 27.927 35.980 1.00 53.89 ATOM 451 CA TYR 31 35.124 27.747 35.600 1.00 54.07 ATOM 472 CA LEU 32 37.594 25.107 34.310 1.00 52.72 ATOM 491 CA SER 33 40.974 24.187 35.600 1.00 49.43 ATOM 510 CA PRO 34 43.864 24.147 33.110 1.00 41.67 ATOM 524 CA PRO 35 44.074 20.337 32.590 1.00 46.11 ATOM 530 CA GLU 36 40.404 20.317 31.650 1.00 30.32 ATOM 545 CA ARG 37 40.464 23.597 29.640 1.00 17.05 ATOM 569 CA LYP 38 43.434 22.497 27.460 1.00 19.61 ATOM 591 CA ARG 39 41.524 19.337 26.310 1.00 21.22 ATOM 615 CA LEU 40 38.184 21.167 25.940 1.00 10.93 ATOM 634 CA ALA 41 39.834 23.657 23.510 1.00 10.81 ATOM 644 CA LYP 42 41.344 20.617 21.670 1.00 20.84 ATOM 666 CA MET 43 38.004 18.787 21.490 1.00 19.62 ATOM 683 CA LEU 44 35.884 21.877 20.620 1.00 16.95 ATOM 702 CA GLN 45 38.504 23.247 18.140 1.00 23.14 ATOM 719 CA LEU 46 38.814 26.507 20.170 1.00 17.31 ATOM 738 CA SER 47 41.784 28.247 21.770 1.00 22.52 ATOM 749 CA GLU 48 42.464 28.237 25.540 1.00 18.67 ATOM 764 CA ARG 49 41.984 32.017 25.510 1.00 22.59 ATOM 788 CA GLN 50 38.484 31.627 24.050 1.00 17.42 ATOM 805 CA VAL 51 37.614 28.917 26.620 1.00 8.87 ATOM 821 CA LYP 52 38.664 31.067 29.630 1.00 15.01 ATOM 843 CA THR 53 37.104 34.267 28.220 1.00 21.29 ATOM 857 CA TRP 54 33.794 32.697 27.320 1.00 15.97 ATOM 881 CA PHE 55 33.164 31.167 30.720 1.00 16.56 ATOM 901 CA GLN 56 34.244 34.267 32.580 1.00 27.30 ATOM 918 CA ASN 57 31.854 36.577 30.640 1.00 31.82 ATOM 932 CA ARG 58 29.204 33.887 30.940 1.00 28.78 ATOM 956 CA ARG 59 29.414 34.027 34.740 1.00 42.57 ATOM 980 CA ALA 60 28.834 37.777 34.520 1.00 52.64 ATOM 990 CA LYP 61 25.674 36.957 32.590 1.00 47.32 ATOM 1012 CA TRP 62 24.714 34.207 35.090 1.00109.93 ATOM 1036 CA ARG 63 25.094 36.337 38.210 1.00145.64 ATOM 1060 CA ARG 64 22.154 38.367 36.850 1.00409.17 ATOM 1084 CA SER 65 19.994 35.337 36.560 1.00567.55 ATOM 1095 CA GLY 66 20.044 34.427 40.200 1.00313.57 ATOM 1110 CA PRO 67 22.124 34.867 43.420 1.00232.72 ATOM 1116 CA SER 68 22.484 31.017 43.640 1.00296.77 ATOM 1127 CA SER 69 26.064 29.747 43.910 1.00746.26 ATOM 1138 CA CGL 70 26.794 26.717 41.750 1.001312.96 TER ENDMDL -- 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] selection of group in do_dssp
Dear gromacs users When I used do_dssp for my protein analysis, gromacs asked me [select a group]. what is the best group for this command? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PBC
Morteza Khabiri wrote: Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for visualization) I have used the following command: trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol but it is not working. Is there any other method or command which I could implement pbc in trajectory. Thanks in advance Morteza Shahab Shariati wrote: You can use other flags of trjconv command as follows: Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center -- 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] helical parameters for DNA
Hi gromacs users I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal 87(6) 3799–3813) inwhich helical parameters for DNA (rise, slide, twist, roll, tilt, shift) calculated by md simulation, but I did not understand two things: How and what command these parameters were calculated? I read gromacs manual. in that there is only g helix and g helixorient for Protein specific analysis. can any body help me how to do this ? -- 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] separation of two strands of DNA during of simulation
Dear Justin thanks for your attention. You said that separation of two strands of DNA during of simulation is a normal consequence of periodic boundary conditions. I had used periodic boundary condition in mdp file as following: Periodic boundary conditions: pbc = xyz Should I delete pbc from mdp file? Whether elimination of pbc prevents separation of two strand of DNA? --- SS -- 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] separation of two strands of DNA during of simulation
Hi gromacs users I runing md simulation of DNA for 20 ns (5000 frame). I see trajectory during simulation. I see in some times, two strands of DNA are seprated. simulation now is in frame of 4600. is this state true and rational? any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulated annealing (SA)
Hi gromacs users 1) after doing simulated annealing simulation, who can I understand that obtained structure is in global minimum and not in local minimum? 2) who can I understand that parameters used in mdp file (annealing_npoints, annealing_time, annealing_temp) are true? Any help will highly appereciated. -- 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] mdp file
Hi gromacs users I want compare simulation of protein with simulation of protein-dna. should conditions (mdp file[T, P, dt, steps, ..] and box size) be same in two simulations? thanks alot -- 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] gen_vel
Hi gromacs users I want to simulation of pr-dna as follows: 1) energy minimization 2) equilibration 3) full md. Should I use gen_vel=yes in mdp files for both (2) and (3) steps? Thank you so much for any help! -- 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] NMR and X-ray structures
Hi gromacs users I want to simulate protein-dna interaction. but pdb file of my protein has 20 models. why pdb structures determined by NMR method consist of several models whereas pdb structures determined by X-RAY diffraction method consist of one model? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rigidn or flexible water models
Hi gromacs users Is TIP3P water model rigid? rigidity means deletion of bonded interactions. is it true? Thank you so much for any help! -- 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] rigid or flexible water models
Dear Justin application of SETTLE algorithm is equal to rigidity. is it true? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force constant for position restraints
Hi gromacs users there is a option in pdb2gmx command : -posrefc (Force constant for position restraints). and also there is following lines in top file: #ifdef POSRES #include posre.itp #endif which of them is better way for position restraint simulation and determining of force constant? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] amber 03 forcefield
Hi gromacs users I will use amber 03 forcefield for simulation of protein-dna interaction. but why ffamber03.atp is as follow : amber99_0 1.00800 ; H0 H aliph. bond. to C with 1 electrwd. group (03GLY) amber99_1 79.9 ; BR bromine amber99_2 12.01000 ; C sp2 C carbonyl group amber99_3 12.01000 ; CA sp2 C pure aromatic (benzene) amber99_4 12.01000 ; CB sp2 aromatic C, 56 membered ring junction amber99_5 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS amber99_6 12.01000 ; CK sp2 C 5 memb.ring in purines amber99_7 12.01000 ; CM sp2 C pyrimidines in pos. 5 6 amber99_8 12.01000 ; CN sp2 C aromatic 56 memb.ring junct.(TRP) amber99_9 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N amber99_1012.01000 ; CR sp2 arom as CQ but in HIS why amber99 instead of amber03? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulated annealing (SA)
Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-dna]. Is there limitation in election of annealing _time? what is optimum value for annealing _time? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulated annealing (SA)
Hi all Simulated annealing consists of heating and gradually cooling steps. What is maximum temperature that we can use for heating in SA simulation of protein. Any help will highly appreciate. -- 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] simulated annealing (SA)
Dear Justin thanks for your attention In mdp file, if annealing_temp and annealing_time values are as follow: annealing_temp = 200 700 600 500 400 300 annealing_time =03040 506070 so, dt and nsteps have to determine such that time of SA simulation be 70. is it true? -- 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] simulated annealing (SA)
Hi all I have some questions about simulated annealing (SA): 1) Is SA a optimization method? or a minimization method? 2) Steps in md simulation are as follow: (a) minimization (b) equilibration (c) production run (d) analysis so, where do SA lie in previous line? (before or after minimization) Thank you so much for any help! -- 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] simulated annealing (SA)
Hi all For simulated annealing simulation, except things mentioned as follow,what things should be in mdp file? integrator dt nsteps annealing annealing npoints annealing time annealing temp tcoupl tc_ grps tau_t ref_ t Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cross-correlations as a function of interatomic distance
Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- 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] g_hbond
I used g_hbond for analysis of hydrogen bonds. g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist -a 30 -r 0.35 Following text was turned up: ACF 288/288 Normalization for c(t) = 0.0204067 for gh(t) = 8.10294e-06 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.685894 +/- 0.00448515 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0199698 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.015 65.068 14.879 0.0199698 Backward0.009108.405 16.144 One-way 0.020 48.818 14.166 Integral0.007143.963 16.847 Relaxation 0.085 11.787 10.644 HB lifetime = 10.98 ps Note that the lifetime obtained in this manner is close to useless Use the -ac option instead and check the Forward lifetime *Is my manner wrong? * * * *What job Should be done?* -- 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] cross-correlations as a function of interatomic distance
Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- 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] energy minimization
Hi gromacs users I want to study interaction of protein-dna by gromacs. For energy minimization, is using of only 1 algorithm, for example steepest descent or conjugate gradient, enough? How many steps is necessary for EM? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] temperature
Hi gromacs users I want to run simulation of protein-dna interaction. what is best for temperature in mdp file: 1) 300K (default) 2) 310k (physiologic temperature) Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] best interval for saving configurations ?
Hi all What is the best interval for saving configurations in full md step? (every what ps?) -- 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] SPC model for water, is suitable for amber03 force field?
Hi all I am beginner in gromacs. I want to simulate interaction between protein and dna. SPC model for water, is suitable for amber03 force field. -- 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] SPC model for water, is suitable for amber03 force field?
Hi all How I can obtain tip3p.itp and tip3p.gro files for amber force field to use them in gromacs program for simulation? there are tip3p.itp and tip3p.gro files in top folder of gromacs which are suitable for gromacs force fields no amber force fields. -- 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] SPC model for water, is suitable for amber03 force field?
Dear Justin thanks for your attention therefore, should I use tip3p.itp file from http://chemistry.csulb.edu/ffamber/ and spc216.gro from top in gromacs program? -- 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] global or local minimum
*Hi ** **after energy minimization step, how can be understand that obtained **structure is in global or local minimum? ** ** * -- 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
