[gmx-users] RE: RE: RE: Doubts over g_lie usage
Thank you so much for your time and explanation. I am recalculating the energy co-ordinates and using it in g_lie calculations. I have read the manual and changed the .mdp file I am using. The following is the mdp file, please check for the correctness. The text in bold font are newly included after your suggestions. Can I use this mdp to calculate the LIE correctly? cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 500 ; total 1 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 500 nstxtcout = 500 nstlist = 10 ns_type = grid rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) vdwtype = cut-off rvdw= 1.4 ; gromos96 force field/ short-range van der Waals cutoff (in nm) ;coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ;fourierspacing = 0.12; grid spacing for FFT ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 4 ;ewald_rtol = 1e-5 *coulombtype = Reaction-Field-zero epsilon_rf = 0* optimize_fft= yes pbc = xyz ; modified Berendsen temperature coupling is on in two groups Tcoupl = V-rescale; modified Berendsen thermostat tc-grps = S04 SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = S04 SOL ; Mode for center of mass motion removal comm-mode = Linear ; Groups for center of mass motion removal comm-grps = System ; Pressure coupling is now on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ~ Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130p5000244.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: RE: Doubts over g_lie usage
Thanks for that explanation. I would like to know this with little more detail. What do you mean by RF-0 and which cut-off value are you talking about? Rerunning the trajectory means the whole MD run again? Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130p5000150.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Doubts over g_lie usage
Hello everyone, I have a doubt about LIE calculation using g_lie in gromacs. This doubt is about the values automatically assigned for -Clj and -Cqq flags when I ran the following command: $ g_lie -f J32_md10ns.edr -o LIE_1A1_J32.xvg -b 7001 -e 1 -ligand J32 The following text contains my options and the values automatically assigned for -Clj and -Cqq :-) g_lie (-: Option Filename Type Description -f J32_md10ns.edr InputEnergy file -o LIE_1A1_J32.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 7001First frame (ps) to read from trajectory -e time 1 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output xvg, xpm, eps and pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -Elj real 0 Lennard-Jones interaction between ligand and solvent -Eqq real 0 Coulomb interaction between ligand and solvent -Clj real 0.181 Factor in the LIE equation for Lennard-Jones component of energy -Cqq real 0.5 Factor in the LIE equation for Coulomb component of energy -ligand string J32 Name of the ligand in the energy file Opened J32_md10ns.edr as single precision energy file Using the following energy terms: LJ:LJ-SR:J32-SOL LJ-LR:J32-SOL LJ-14:J32-SOL Coul: Coul-SR:J32-SOL Coul-14:J32-SOL Back Off! I just backed up LIE_1A1_J32.xvg to ./#LIE_1A1_J32.xvg.3# Last energy frame read 1 time 1.000 DGbind = -49.210 (5.282) More questions are 1. Is the DGbind value here is the overall average of LJ and Coul ? 2. If that is the case how can I calculate individual average values for LJ and Coul? 3. How are the 0.181 and 0.5 values for -Clj and -Cqq assigned? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Doubts over g_lie usage
Dear Tom, The explanation really helps me understand LIE much more clearer. What's the issue if I have used PME coulombtype? I have actually used PME. Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130p5000146.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: tutorials for Coarse-Grained MD Simulation
Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How do I do this step.? These files are also tested with Gormacs 3.3.1 version, how do they work with recent versions of GROMACS? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p492.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: tutorials for Coarse-Grained MD Simulation
Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the available Martini files and programs with the recent version of GROMACS that is version 4? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p486.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] tutorials for Coarse-Grained MD Simulation
Dear Gromacs Users, I would like to know if there are any tutorials for Coarse-Grained MD Simulation available anywhere. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] LIE using g_lie
Dear colleagues, I have some doubts about LIE and would like some clarifications. While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol and a standard deviation in parentheses. How well can I use this value alone or meaningful it is by itself in comparing the binding affinity of a set of ligands (not calculating the same for the ligand-only system) ? Another query is that, to calculate the DGbind using the following formula DGbind = vdw_bound - vdw_free + Elec_bound - Elec_free Are the values calculated by -Clj tag is the value for vdw_bound or vdw_free and -Cqq is for Elec_bound or Elec_free? In another literature, this formula is further detailed DGbind_formula http://gromacs.5086.n6.nabble.com/file/n444/DGbind.jpg where alpha, beta and gamma values are also needed, what are these values and how to calculate them? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/LIE-using-g-lie-tp444.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Linear Interaction energy calculations
Dear colleagues, Thanks for opening up this topic. I also have some doubts about LIE and would like some clarifications. While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol and a standard deviation in parentheses. How well can we use this value alone or meaningful it is by itself, not calculating the same for the ligand alone, in comparing the binding affinity of a set of ligands? Another query is that, to calculate the DGbind using the following formula DGbind = vdw_bound - vdw_free + Elec_bound - Elec_free Are the values calculated by -Clj tag is the value for vdw_bound or vdw_free and -Cqq is for Elec_bound or Elec_free? In another literature, this formula is further detailed http://gromacs.5086.n6.nabble.com/file/n424/DGbind.jpg where alpha, beta and gamma values are also needed, what are these values and how to calculate them? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Linear-Interaction-energy-calculations-tp4999882p424.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, Thanks for that information. I also would like to confirm with you that should I combine my metal ion too while I combine Protein and POPC into Protein_POPC group to be used in COMM removal? So that I will have a group Protein_HEM_POPC. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999759.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: question about minimisation
Hi, Did you call your genrestr output in your mdp file using define = * ? (for example define = -DPOSRES ; where posres was your file name.) Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/question-about-minimisation-tp4999681p4999685.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Thanks for that comment. I've another query during inflating step in Justin's tutorial. In my case, during the inflation, 4 lipids from the upper and 2 lipids from the lower leaflets were removed. Would there be a problem in this sort non-uniform deletion (I mean like 4 from upper and 4 from lower)? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999633.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, Thanks for all your help to get me through membrane simulations. I've a problem to be solved. I need a long and thick membrane to simulate a big protein. The longest bilayer that I can download from Tieleman's website is 64 molecules long. How can I make (double or triple the bilayer) a long and thick bilayer to accommodate a large protein? Are there any experimental evidence about the thickness of the membrane that should be followed before expanding the membrane? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999602.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Thank you so much for that, Justin. Now I could expand the bilayer. I've another query. My protein has a small N-terminal portion embedded in the membrane, I would like to insert only this part into the membrane during 'packing the lipid around the protein' step in your tutorial. Initially I was trying to do simulation only with this TM region and then attaching the rest of the protein with this TM region and simulate the whole system. But was time-taking. Can you please guide me to pack the lipid bilayer only around a 33-residues long peptide in my protein and rest with water? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999605.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, That works really fine and thanks. Now, how can I add additional SOL molecules only one side of the bilayer (either upper or lower)? Since my protein binds at the outer side (extracellular region) of the membrane I can only fill the upper (extracellular) region with SOL molecules instead of adding them also inside the membrane, to reduce the system size ? Can we do magic here with any commands to add SOL molecules only single side of the membrane? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999625.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, I have the following Notes during NPT equilibration. NOTE 1 [file pr_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 What do they really mean? Is the system safe with these notes? Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999483.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, I have another doubt on the strong posres that was included in the topology file. When do we need to remove that position restraint? Does it really affect at point of time the system? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999401.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Thanks Justin, The explanations are very very useful during my course of simulating a protein with POPC. I also would like to get explanation on how to simulate a protein which has only its N-terminal region embedded in the membrane but the rest in solvent. What is the easy and accurate way to do it? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999409.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, Thanks for the effort to help me. I still no out of the error. The following is the content of my topol_popc.top ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; Include ion topologies #include gromos53a6_lipid.ff/ions.itp ; System specifications [ system ] 128-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 128 SOL 2460 And the following is the first part of my popc128b.gro file Alm on surf + relaxed popc 14036 1POP C11 0.253 5.425 1.688 1POP C22 0.428 5.314 1.792 1POP C33 0.334 5.243 1.571 1POP N44 0.378 5.352 1.660 1POP C55 0.474 5.439 1.590 1POP C66 0.606 5.390 1.531 1POP O77 0.692 5.366 1.643 1POP P88 0.834 5.316 1.587 1POP O99 0.800 5.197 1.505 1POPO10 10 0.903 5.435 1.533 1POPO11 11 0.890 5.266 1.729 1POPC12 12 0.823 5.142 1.753 1POPC13 13 0.836 5.086 1.895 1POPO14 14 0.766 4.964 1.924 1POPC15 15 0.632 4.959 1.944 1POPO16 16 0.555 5.019 1.869 1POPC17 17 0.589 4.833 2.020 1POPC18 18 0.615 4.703 1.944 1POPC19 19 0.595 4.575 2.025 1POPC20 20 0.625 4.467 1.920 1POPC21 21 0.677 4.340 1.987 1POPC22 22 0.813 4.357 2.055 1POPC23 23 0.848 4.223 2.120 1POPC24 24 0.884 4.121 2.012 1POPC25 25 0.957 4.013 2.043 1POPC26 26 0.994 3.986 2.189 1POPC27 27 1.069 3.853 2.202 1POPC28 28 0.967 3.739 2.204 1POPC29 29 1.012 3.593 2.202 1POPC30 30 0.916 3.478 2.169 1POPC31 31 0.869 3.518 2.029 1POPC32 32 0.801 5.205 1.983 . . . . . What are the parts mismatching in these files? Since it says the atom names from the top file will be used, is it safe to ignore this warning too? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999354.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, Thanks for the suggestion I got it solved somehow. The main problem was in the popc128b.pdb itself, it has first 64 lipids and half of the SOl molecules followed by rest of the POPC and SOL molecules. When I rearranged them the error was solved. But now another thing I would like to confirm with you. During shrinking stage, I get the following notes, please tell me are they OK at this stage, NOTE 1 [file topol.top, line 3070]: System has non-zero total charge: 5.00e+00 Analysing residue names: There are:46Protein residues There are: 126 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 21063.00 Largest charge group radii for Van der Waals: 0.249, 0.247 nm Largest charge group radii for Coulomb: 0.249, 0.247 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 160x160x48, spacing 0.110 0.114 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file em_st.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 17 Mb of data There were 2 notes Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999391.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Hi Justin, I followed your comments and now at the stage of adding solvents. I wonder to see the protein after shrinking step to have no SOL molecules as there were SOL molecules in the source popc128b.pdb. Had we removed all the original SOL molecules anywhere during the course of tutorial? I also see one of the POPC molecules standing out (upside down) of the bilayer area. How would that be adjusted? http://gromacs.5086.n6.nabble.com/file/n4999393/POPC..jpg Thanks Peterson -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999393.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer
Thanks for the comment. By the way how to make a bigger box at this time of the tutorial without affecting any part of the system. Can I use editconf with slightly bigger number for z-axis (something like 6.7 which was 5.7 before)? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999395.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Error in Membrane simulations with POPC bilayer
Hi Justin and Anirban, I started a membrane simulation with POPC bilayer after a training with the given KALP peptide and DPPC bilayer. I am following both of your tutorials (mainly the Justin's). I have problem at where I generate a .tpr file for a DPPC (POPC here)-only system using grompp. I see another warning on non-matching number of atoms along with the error that you recommended a safe one. My error is Warning: atom name 3340 in topol_popc.top and popc_128b_H.pdb does not match (C12 - H2) Warning: atom name 3341 in topol_popc.top and popc_128b_H.pdb does not match (C13 - O) Warning: atom name 3342 in topol_popc.top and popc_128b_H.pdb does not match (O14 - H1) Warning: atom name 3343 in topol_popc.top and popc_128b_H.pdb does not match (C15 - H2) Warning: atom name 3344 in topol_popc.top and popc_128b_H.pdb does not match (O16 - O) Warning: atom name 3345 in topol_popc.top and popc_128b_H.pdb does not match (C17 - H1) Warning: atom name 3346 in topol_popc.top and popc_128b_H.pdb does not match (C18 - H2) Warning: atom name 3347 in topol_popc.top and popc_128b_H.pdb does not match (C19 - O) Warning: atom name 3348 in topol_popc.top and popc_128b_H.pdb does not match (C20 - H1) (more than 20 non-matching atom names) WARNING 1 [file topol_popc.top, line 26]: 10708 non-matching atom names atom names from topol_popc.top will be used atom names from popc_128b_H.pdb will be ignored Analysing residue names: There are: 128 Other residues There are: 2460 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 42105.00 Largest charge group radii for Van der Waals: 6.115, 5.932 nm Largest charge group radii for Coulomb: 6.546, 6.115 nm WARNING 2 [file em_st.mdp]: The sum of the two largest charge group radii (12.661407) is larger than rlist (0.90) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 54x56x48, spacing 0.117 0.117 0.119 Estimate for the relative computational load of the PME mesh part: 0.45 This run will generate roughly 34 Mb of data There were 2 warnings --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1563 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Can any one of you help me move from here? Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] MD simulation with varying pH
Dear GROMACS Users, I'm planning to work on a protein that activates itself under lower pH conditions. And I don't have any clues how to do it in GROMACS. My first question is about the possibilities to do this in GROMACS, has anyone done this before? It can even be a constant simulations at a particular lower/higher pH or gradually lowering/increasing pH. Any suggestion on this would give me a lead. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/MD-simulation-with-varying-pH-tp4999095.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] AMBER heme parameters to simulate in GROMACS
Dear colleagues, Has anyone run simulation with heme moiety in GROMACS with AMBER FF before? I have a problem running it. I need the topology parameters for the heme. Thanks Peterson -- View this message in context: http://gromacs.5086.n6.nabble.com/AMBER-heme-parameters-to-simulate-in-GROMACS-tp4962588.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Fwd: HEME-cysteine gromacs simulation
Zhang Bing, I guess it is problem in your visualizers. Try to label the atom using VMD which goes well with most of the file types derived in GROMACS. I hope you'll see the atom as FE not just F. Thanks Peterson -- View this message in context: http://gromacs.5086.n6.nabble.com/Fwd-HEME-cysteine-gromacs-simulation-tp4957846p4962257.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
