Re: [gmx-users] Simulation of membrane protein
Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problems with g_membed tools
I used the mdp file listed previously to generate the tpr file. It gave this warning: WARNING 1 [file membed.mdp]: Can not exclude the lattice Coulomb energy between energy groups then I ignored the warning with -maxwarn 1 and gave the tpr file to g_membed, command line like this: g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000 Then it seems the g_membed did one iteration and stopped , it returned this: Back Off! I just backed up step1b.pdb to ./#step1b.pdb.2# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.2# Wrote pdb files with previous and current coordinates --- Program g_membed, VERSION 4.5.3 Source code file: nsgrid.c, line: 540 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am wondering if it is because the parameters in the mdp file set improper. How to change it? Linda Does this mean that I need to 2011/11/11 Mark Abraham mark.abra...@anu.edu.au: On 11/11/2011 5:13 PM, LindaSong wrote: Thank you very much for your reply, Mark It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this: [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_A2 1 POPC 256 This problem solved. But then comes a new one. When I did the g_membed, the system blowed up after one iteration! I think I really shouldn't ignore the warning from the grompp. However, as an inexper ienced user, I don't know how to improve the mdp file. Can you give me any hint? Use a text editor that writes plain text. Junk nbsp; throughout cannot help things. As before, reporting the actual text of the warning is critical to working out what might be wrong. Mark The mdp file for the g_membed is like this: cpp = /lib/cpp ; Run parameters integrator = md nsteps = 1000 dt = 0.002 ; Output control nstxout = 10n bsp; nstvout = 10 nstenergy = 10 nstlog = 10 ; Bond parameters continuation = no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 1 rlist = 1.4 rcoulomb = 1.4 rvdw nb sp; = 1.4 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 nbsp; ref_t = 300 300 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.0 compressibility = 4.5e-5 4.5e-5 ref_p ; = 1.0 1.0 ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; Energy monitoring energygrps = Protein ; Non-equilibrium MD freezegrps = Protein freezedim nb sp; = Y Y Y ; Energy group exclusions energygrp_excl = Protein Protein Thanks a lot! Linda -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Charged wall
Hi Gmx Users, I am wondering whether is it possible in Gromacs to build sth like a charged wall to which the last residue of my terminal protein will be attached and run the simulation? I mean that the protein cannot move through some border which is attached to and which is positively or negatively charged. Thank you Steven -- 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] pull_distance
hi all. I need your advice. I have marked several atoms from one chain and several atoms from another chain (about 8 from each chain), they are forming 5 h-bonding places, and now I want to stabilize the distance between this chains during the MD. Can I use com pulling distance Y Y Y for it with pull_k1 = 2000 and pull_init1 = with pull_rate1 = 0? Will it hold the initial distance all the time and how many groups I have to create? Will it be enough 2 groups (one with a selected atoms from first chain and another with atoms from the second) in the index file or I have to create sveral groups which will consist of a pairs of groups of atoms involved in h-bonding? As I understood in this way I will handle a center of mass, so the first variant is preferable. Is it true? Thank you for responce -- * Nemo me impune lacessit* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Insertion of the protein into membrane with Gmembed
James Starlight wrote: Dear Gromacs Users! I have some questions about insertion protein into membrane with Gmembed 1) I've used default parameters from gmembed manual for preparing input for insertion integrator = md energygrp = Protein freezegrps = Protein freezedim = Y Y Y energygrp_table energygrp excl = Protein Protein Here Protein is my protein group in topology.top I've obtained 2 warning from gropp WARNING 1 [file gmembed.mdp, line 27]: Unknown left-hand 'energygrp' in parameter file WARNING 2 [file gmembed.mdp, line 27]: Unknown left-hand 'energygrp excl' in parameter file What does it means ? If I ignore those warnings I've obtain Both of the warnings indicate typographical errors. Please see the manual for proper keywords. -Justin No energy groups defined. This is necessary for energy exclusion in the freeze group May be I should define freezegrps as my lipid group not a protein or use ndx file as an alternative ? Thanks, James -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: mdp file problem
madhumita das wrote: Dear Justin, I could solve that perticular error but another problem has come, After running energy minimization, the sulphur and mercury(GG)atoms (present in the modified residue of cysteine named CYP at 182 position) break the bonds. Bonds don't break and form during molecular mechanical processes. Likely whatever you're seeing is simply extreme instability in the system. Most likely your topology is wrong. You haven't said what parameters you're using, but as I know I have indicated previously, deriving good parameters for such an exotic species will be extremely challenging for the biomolecular force fields present in Gromacs. My guess is that you haven't yet obtained proper parameters. -Justin On Thu, Nov 10, 2011 at 7:28 PM, madhumita das madhumita.bioi...@gmail.com mailto:madhumita.bioi...@gmail.com wrote: Dear Justin, I could resolve that perticular error but another problem has come, After running energy minimization, the sulphur and mercury(GG)atoms (present in the modified residue of cysteine named CYP at 182 position) break the bonds and become freely moving atoms. I have attached my prepared gromacs(aqp_newbox) topology(topol.top) and file obtained after energy mimization(em.gro). Please help me. Madhumita On Tue, Nov 8, 2011 at 5:03 PM, madhumita das madhumita.bioi...@gmail.com mailto:madhumita.bioi...@gmail.com wrote: Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , following error comes. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 5000 Step= 17, Dmax= 1.5e-06 nm, Epot= 9.89827e+17 Fmax= inf, atom= 2700 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. writing lowest energy coordinates. Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax 1000. Potential Energy = 9.8982703e+17 Maximum force =inf on atom 2700 Norm of force = 1.7474532e+19 The mdp file is attached. Please help. Madhumita Das -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately. On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pull_distance
Алексей Раевский wrote: hi all. I need your advice. I have marked several atoms from one chain and several atoms from another chain (about 8 from each chain), they are forming 5 h-bonding places, and now I want to stabilize the distance between this chains during the MD. Can I use com pulling distance Y Y Y for it with pull_k1 = 2000 and pull_init1 = with pull_rate1 = 0? Will it hold the initial distance all the time and how many groups I have to create? Will it be enough 2 groups (one with a selected atoms from first chain and another with atoms from the second) in the index file or I have to create sveral groups which will consist of a pairs of groups of atoms involved in h-bonding? As I understood in this way I will handle a center of mass, so the first variant is preferable. Is it true? Yes. Create one group for pull_group0, which is the reference (probably arbitrary in this case) and another for pull_group1. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297323; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297323; Does thic correct for both NPT and NVT ensembles ? James 2011/11/11 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately. On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297323; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297323; Does thic correct for both NPT and NVT ensembles ? It is incorrect to set different groups at different temperatures. Whatever result you obtain would be completely unrealistic. -Justin James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately. On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
Justin, What temperature for NVT phase should be in gen_temp= 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297297 for protein in DMPC bilayer. The bilayer with water parts diffused in up and down direction of the box relative protein Why this should occur ? Might I alpy posres for lipid in NVT phase ? 2011/11/11 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297323; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297323; Does thic correct for both NPT and NVT ensembles ? It is incorrect to set different groups at different temperatures. Whatever result you obtain would be completely unrealistic. -Justin James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately. On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**
Re: [gmx-users] orca question and LA
Dear Sir: I want to know version of groamcs and orca in your the qm/mm calculation? are they in parallel ? thank you! --- 11年11月10日，周四, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午7:35 I hope you mean ./configure --with-qmmm-orca --without-qmmm-gaussian etc. http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html www.google.com etc. For MPI, I can't really say as I did not get qm/mm with orca/gmx to run in parallel yet (using cp2k atm). Maybe someone else can advise you. Cheers, Micha On 10/11/11 10:49, xi zhao wrote: I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi then make make install are it right? --- 11年11月10日，周四, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午4:47 Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Justin, What temperature for NVT phase should be in gen_temp= 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297297 for protein in DMPC bilayer. You should generate velocities for the temperature you wish to use. Otherwise, equilibration will take longer than necessary. At worst, it may crash if your system is far from equilibrium as the temperature coupling algorithm may fail. The bilayer with water parts diffused in up and down direction of the box relative protein Why this should occur ? Might I alpy posres for lipid in NVT phase ? Given that I know nothing about the magnitude of such motion, I can't really say. If there are severe distortions or displacements, restraining headgroup atoms may be necessary for the initial phases of equilibration. Usually such restraints should not be necessary for most well-built systems. -Justin 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297323; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297323; Does thic correct for both NPT and NVT ensembles ? It is incorrect to set different groups at different temperatures. Whatever result you obtain would be completely unrealistic. -Justin James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately. On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] Charged wall
You could create an atomistic charged wall by placing atoms in a plane or grid and using position restraints or freeze groups to keep them in place. You could them use the pull code to restrain part of the protein relative to an atom(s) in this atomistic wall. You could obtain your desired charge distribution by using a combination of helium and sodium or chloride atoms. Alternatively, you could create a new atom type with a fractional charge and whatever LJ parameters you want. Of course, you could also construct a more atomistically realistic wall.Some people have done similar things to study proteins absorbed onto electrodes: http://pubs.acs.org/doi/abs/10.1021/ja910707r http://www.sciencedirect.com/science/article/pii/S0013468609003119 Chris. -- original message -- Hi Gmx Users, I am wondering whether is it possible in Gromacs to build sth like a charged wall to which the last residue of my terminal protein will be attached and run the simulation? I mean that the protein cannot move through some border which is attached to and which is positively or negatively charged. Thank you Steven -- 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] GROMACS/ORCA QMMM
Dear GROMACS users, I'm trying to run a QM-MM optimization. I solvate my protein and add ions then I do a classical optimization (just GROMACS). After that I run grompp with the following minim.mdp file (just showing qmmm options): QMMM= yes QMMM-grps = Other QMmethod= RHF QMbasis = 3-21G QMMMscheme = Oniom QMcharge= -1 QMmult = 1 SH = no This creates the *.tpr file that use to run mdrun. I use the following *.ORCAINFO file: !PAL8 Quick-DFT VerySlowConv %scf Maxiter 300 end %pal nprocs 8 end The ORCA run quickly converges but after that mdrun run stops with a segmentation fault. Am I missing something in all of this? Any help would be greatly appreciated. Thanks Jose Tusell -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
Justin, It was a huge bilayer replacement on the magnitude comparable with the protein size. In more detailes both of the lipid leflets moved to the top and bottom side of the pb. The protein were placed on the old place ( due to the posres) so it turned out isolated from membrane :) Also I've found that I could use simulated annealing to slowly warm the system under *NPT* conditions So in this case could I skip the nvt phase and do this mod NPT equilibration ? also I've create posres for the lipid on Z direction only. I hopes this helps prevent such bilayer diffusion. James 2011/11/11 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, What temperature for NVT phase should be in gen_temp= 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297297 for protein in DMPC bilayer. You should generate velocities for the temperature you wish to use. Otherwise, equilibration will take longer than necessary. At worst, it may crash if your system is far from equilibrium as the temperature coupling algorithm may fail. The bilayer with water parts diffused in up and down direction of the box relative protein Why this should occur ? Might I alpy posres for lipid in NVT phase ? Given that I know nothing about the magnitude of such motion, I can't really say. If there are severe distortions or displacements, restraining headgroup atoms may be necessary for the initial phases of equilibration. Usually such restraints should not be necessary for most well-built systems. -Justin 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297323; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297323; Does thic correct for both NPT and NVT ensembles ? It is incorrect to set different groups at different temperatures. Whatever result you obtain would be completely unrealistic. -Justin James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a symmetrical protein should delete an equal number of lipids from each leaflet, if the geometry of the top and bottom leaflets is comparable. Either try placing the protein at a different location to achieve equivalent removal or manually delete a lipid and be sure to equilibrate adequately. On Inflategro's sites I havenot found such specifity for above parameters for different bilayers :( The cutoffs specified are simple grid search parameters. They do not necessarily need to be altered depending upon the lipid type. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Justin, It was a huge bilayer replacement on the magnitude comparable with the protein size. In more detailes both of the lipid leflets moved to the top and bottom side of the pb. The protein were placed on the old place ( due to the posres) so it turned out isolated from membrane :) If the bilayer is splitting across periodic boundaries (I'm assuming that's what you mean by pb), then it's more likely that you placed the components of your system in an inconvenient way than it is that something is actually wrong. Also I've found that I could use simulated annealing to slowly warm the system under /NPT/ conditions So in this case could I skip the nvt phase and do this mod NPT equilibration ? Prepare the system in whatever manner is defensible and sensible. Normally one deals with temperature before pressure for stability issues. If you have found a justifiable protocol that leads to a stable simulation, use it. -Justin also I've create posres for the lipid on Z direction only. I hopes this helps prevent such bilayer diffusion. James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, What temperature for NVT phase should be in gen_temp= 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297297 for protein in DMPC bilayer. You should generate velocities for the temperature you wish to use. Otherwise, equilibration will take longer than necessary. At worst, it may crash if your system is far from equilibrium as the temperature coupling algorithm may fail. The bilayer with water parts diffused in up and down direction of the box relative protein Why this should occur ? Might I alpy posres for lipid in NVT phase ? Given that I know nothing about the magnitude of such motion, I can't really say. If there are severe distortions or displacements, restraining headgroup atoms may be necessary for the initial phases of equilibration. Usually such restraints should not be necessary for most well-built systems. -Justin 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some system groups in index.ndx ) For my system composed of protein dmpc and water : ref_t = 323 297323; Does all this values in mdp file must be equal ( to the temperature of the lipid phase transition) ref_t = 297 297297 or each value must correspond to the temperature of phase transition of the individual element ? ref_t = 323 297323; Does thic correct for both NPT and NVT ensembles ? It is incorrect to set different groups at different temperatures. Whatever result you obtain would be completely unrealistic. -Justin James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but inflategro deleate 2 lipid from upper and just 1 from lower layer. It's strange because I suppose that equal bilayer molecules would be removed :o The number of lipids that are removed will depend on the starting configuration of the membrane and thus where lipids are relative to the protein. Theoretically, a
Re: [gmx-users] Simulation of membrane protein
Justin, 2011/11/11 Justin A. Lemkul jalem...@vt.edu If the bilayer is splitting across periodic boundaries (I'm assuming that's what you mean by pb), then it's more likely that you placed the components of your system in an inconvenient way than it is that something is actually wrong. Bilayer has moved on Z-dimension in periodic box. That is actually what's happend :) http://i1209.photobucket.com/albums/cc394/own11/vmdscene.gif By the way I'ts intresting that Gmembed has removed 6 lipids in comparison to the inflateglo ( althought I've done all things in accordance to the KALP tutorial because my protein is the same). James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Justin, 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu If the bilayer is splitting across periodic boundaries (I'm assuming that's what you mean by pb), then it's more likely that you placed the components of your system in an inconvenient way than it is that something is actually wrong. Bilayer has moved on Z-dimension in periodic box. That is actually what's happend :) http://i1209.photobucket.com/albums/cc394/own11/vmdscene.gif How large of a void exists between your lipids and water prior to starting the simulation? I'm almost certain that you built the unit cell incorrectly - there should never be that much free space. By the way I'ts intresting that Gmembed has removed 6 lipids in comparison to the inflateglo ( althought I've done all things in accordance to the KALP tutorial because my protein is the same). Different algorithms, different results. Nothing odd about that to me. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
Justin, The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle) But after nvt simulation this discrepancy occured :) I've used pbc size like in the KALP simulation because I have bilayer ( 128 lipids) and the protein (38 a.a) of the same size. My box vectors were 6.500 6.500 6.500 Do you think that I should use smaller pbc? How I could define pbc on the right size for my purely bilayer system? I've used trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact at the preequilibrated bilayer and than done anything in accordance to the KALP tutorial James 2011/11/11 Justin A. Lemkul jalem...@vt.edu How large of a void exists between your lipids and water prior to starting the simulation? I'm almost certain that you built the unit cell incorrectly - there should never be that much free space. By the way I'ts intresting that Gmembed has removed 6 lipids in comparison to the inflateglo ( althought I've done all things in accordance to the KALP tutorial because my protein is the same). Different algorithms, different results. Nothing odd about that to me. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Justin, The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle) But after nvt simulation this discrepancy occured :) I've used pbc size like in the KALP simulation because I have bilayer ( 128 lipids) and the protein (38 a.a) of the same size. KALP-15 has only 15 residues; your peptide is significantly longer. My box vectors were 6.500 6.500 6.500 Do you think that I should use smaller pbc? How I could define pbc on the right size for my purely bilayer system? You shouldn't use the box vectors I did in the tutorial - use the dimensions present in the actual membrane you're using. I still see no conceivable way that the bilayer separated that much during NVT without significant empty space in the unit cell to start. In NVT, the volume is constant, so if there are voids, the lipids will fill to expand them. I've seen it countless times, so please be sure you're actually providing sufficient solvent and an appropriate location for all your components within the unit cell. -Justin I've used trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact at the preequilibrated bilayer and than done anything in accordance to the KALP tutorial James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu How large of a void exists between your lipids and water prior to starting the simulation? I'm almost certain that you built the unit cell incorrectly - there should never be that much free space. By the way I'ts intresting that Gmembed has removed 6 lipids in comparison to the inflateglo ( althought I've done all things in accordance to the KALP tutorial because my protein is the same). Different algorithms, different results. Nothing odd about that to me. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_wham and entropic subtraction
Hi, I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_wham and entropic subtraction
On 2011-11-11 21:29, Sanku M wrote: Hi, I just wanted to check whether g_wham ( in gromacs4.5.4) already subtractthe entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku If it does not say so explicitly (and it does not when using g_wham -h) it does not. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] UNK not found in residue topology
Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognized? (I built my own hydrocarbon strucutre and added it to an existing PDB file). Thanks, Adrianna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] UNK not found in residue topology
Janowicz, Adrianna C. wrote: Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognized? (I built my own hydrocarbon strucutre and added it to an existing PDB file). I think you need to be a bit more specific about what you're trying to do. Are you getting errors from pdb2gmx or some other tool? If so, what are they? Otherwise, the only requirement for proper processing is that the PDB format be retained and that the atom names match what is expected in the .rtp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive potential energy for TFE solvent
On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? You probably have atomic overlaps from your choice of cubic 0.516 box earlier. Did you look at the results of genconf before computing with them? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] B-factor to large? Input for TLS
Hi Mark, Thanks for your reply. I will check if the reference structure and the trajectory fit. Cheers Henrey On Mon, Nov 7, 2011 at 9:15 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 5/11/2011 11:05 AM, Henri Mone wrote: Dear Gromacs Users and Experts, I want to calculate from my xtc trajectory the B-factor and the anisotropic temperature factor. I'm using following gromacs command: $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb Does this reference structure in -s make sense for the trajectory supplied for -f? If the computed atomic deviations make no sense, then neither will the fluctuations. I have no idea if g_rmsf takes proper account of periodicity, but you might need either to massage the trajectory suitably with trjconv (see website for suggested workflows), or supply a .tpr with the correct box information. I want to input the resulting PDB file to the TLS Server [1] to calculate the hinge residues for my system. The B-factor which g_rmsf is calculating seem to be to large, they are in the range of 2000 to 6000 (last column without the 1.00 prefix) [2]. The website [3] suggests that a reasonable B-factor should is in the range of 21 to 200. Also the TLS server [1] complains that the b-factors are in the wrong range. I did several test but I have no idea what Im doing wrong. The trajectory is with 250ns long enough to get for my small system a convergence on the B-factor. - I thought it could be a unit problem, what are the B-factor units which g_rmsf uses? Could this cause such an huge difference in the b-factor? g_rmsf converts to Angstroms before writing B-factor output to PDB, as you would expect. Mark - What is the standard unit for the b-factor in the PDB definition (from the PDB database)? - What is a realistic range for the b-factor? - What else could be the error source, what am I doing wrong? Thanks, any help is welcome, Henrey ---1: TLSMD SERVER http://skuld.bmsc.washington.edu/~tlsmd/ ---2: bfac2.pdb : ... ATOM 6146 N GLY 435 97.841 52.072 37.712 1.006712.85 ATOM 6147 HN GLY 435 97.972 52.020 37.437 1.006676.79 ATOM 6148 CA GLY 435 97.953 52.003 37.883 1.006739.30 ATOM 6149 HA1 GLY 435 97.975 51.822 37.563 1.006956.61 ATOM 6150 HA2 GLY 435 97.554 52.041 37.972 1.007042.78 ATOM 6151 C GLY 435 98.601 52.111 38.350 1.006210.20 ATOM 6152 O GLY 435 98.552 51.909 38.905 1.006278.92 ATOM 6153 N ASN 436 99.235 52.437 38.127 1.005772.75 ATOM 6154 HN ASN 436 99.262 52.602 37.668 1.005803.67 ATOM 6155 CA ASN 436 99.904 52.574 38.508 1.005343.12 ATOM 6156 HA ASN 436 99.947 52.400 38.918 1.005671.18 ATOM 6157 CB ASN 436 100.537 52.527 37.948 1.005355.63 ATOM 6158 HB1 ASN 436 100.960 52.556 38.127 1.005098.00 ATOM 6159 HB2 ASN 436 100.553 52.657 37.601 1.005272.78 ATOM 6160 CG ASN 436 100.587 52.258 37.586 1.006031.62 ATOM 6161 OD1 ASN 436 100.582 52.138 37.675 1.006435.18 ATOM 6162 ND2 ASN 436 100.641 52.163 37.176 1.006306.09 ATOM 6163 1HD2 ASN 436 100.689 51.993 36.928 1.006834.63 ATOM 6164 2HD2 ASN 436 100.652 52.264 37.117 1.006062.64 ATOM 6165 C ASN 436 99.947 53.023 38.917 1.004590.56 ATOM 6166 O ASN 436 99.651 53.240 38.597 1.004290.70 ... ---3: B-factor range at 3 Å resolution http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/ -- 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: Using CHARMM 36 for DPPC simulation
Hi Everyone, I did another simulation where i found the the DPPC area per lipid is 0.61 nm^2 . Is this acceptable ? I have seen issues like this on the mailing list before can one of the experts give me some hints. Amit On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey kgp.a...@gmail.com wrote: 5Hello all, I am trying to use CHARMM 36 for DPPC membrane simulation. I did the following so far: 1. Download pdb file containing 128 DPPC molecules from http://www.charmm-gui.org/?doc=archivelib=lipid_pure 2. I separated one lipid molecule from the obtained pdb file and used pdb2gmx -f 1dppc.gro -nochargegrp The top file obtained was converted to itp file by commenting few things out. 3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer from CHARMM GUI for the box length. I used editconf to convert the pdb to gro and manually inserted the box size in the gro file. 4. Created a system.top file which looks like #include charmm36.ff/forcefield.itp #include lipid.itp #include charmm36.ff/tips3p.itp [ system ] chol [ molecules ] DPPC 128 SOL 3659 5. I used following mdp settings integrator = md ; leap-frog integrator nsteps = 2000 ; 40 ns dt = 0.002 ; 2 fs ; Output control nstxout = 10 ; save coordinates every 200 ps nstvout = 10 ; save velocities every 200 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 vdwtype = switch rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw_switch = 0.8 ; Electrostatics rcoulomb= 1.0 rcoulomb_switch = 0.0 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 6 ; cubic interpolation fourierspacing = 0.15 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = DPPC SOL ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 323.15 323.15 ; 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 = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = No ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes gen_temp= 200.0 gen_seed= 173529 ; COM motion removal nstcomm = 1 comm-mode = Linear comm-grps = DPPC SOL ; Energy monitoring energygrps = DPPC SOL ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy The resulting simulation gave me an area per lipid =0.591 nm^2. This is not quite right. Can somebody suggest what else could i do it get close to the 0.63 nm^2 value. Also when i looked at trajectory file it seemed that the box length was not set up quite right because the downloaded pdb file looked ok with the membrane in the middle but at the next frame the membrane was at a totally different location. The leaflets were separated and the middle of the membrane was at the edge of the box. Also when i used pdb2gmx -nochargegrp on the downloaded file it created a gro file whose system size was 8.20170 8.64120 6.54740 in contrast to6.4 6.4 6.38452 . Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
Justin, Indeed GenBox added insufficien of the SOL to my system due to the ussage of increased vdvdat ( I've used 0.350 value for the c atoms only but the were alot of void beetwen water and bilayer ) lipid_posres in Z directions have prevented the displacement of the bilayer but the water were distruibuted irregular on the bilayer surface at the end of NVT phase By the way in Gmembed system I have no such problems because the were no need to use genbox but during processing of the system I've obtain warning WARNING 1 [file membed.mdp]: Can not exclude the lattice Coulomb energy between energy groups What does it mean? By the way could I indicate Area per lipid during processing of my system with the G_membed? James 2011/11/11 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle) But after nvt simulation this discrepancy occured :) I've used pbc size like in the KALP simulation because I have bilayer ( 128 lipids) and the protein (38 a.a) of the same size. KALP-15 has only 15 residues; your peptide is significantly longer. My box vectors were 6.500 6.500 6.500 Do you think that I should use smaller pbc? How I could define pbc on the right size for my purely bilayer system? You shouldn't use the box vectors I did in the tutorial - use the dimensions present in the actual membrane you're using. I still see no conceivable way that the bilayer separated that much during NVT without significant empty space in the unit cell to start. In NVT, the volume is constant, so if there are voids, the lipids will fill to expand them. I've seen it countless times, so please be sure you're actually providing sufficient solvent and an appropriate location for all your components within the unit cell. -Justin I've used trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact at the preequilibrated bilayer and than done anything in accordance to the KALP tutorial James 2011/11/11 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu How large of a void exists between your lipids and water prior to starting the simulation? I'm almost certain that you built the unit cell incorrectly - there should never be that much free space. By the way I'ts intresting that Gmembed has removed 6 lipids in comparison to the inflateglo ( althought I've done all things in accordance to the KALP tutorial because my protein is the same). Different algorithms, different results. Nothing odd about that to me. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**
[gmx-users] picking out resident water molecule?
Hi everyone, I am doing MD simulation with a protein-ligand system, and I want to pick out the water molecules (their residue numbers or coordinates in any frame) that simultaneously contact (within 0.4 nm range for heavy atoms) the ligand and the protein, so that I could plot the lifetime of these resident water molecules within a trajectory. Does anyone know how to achieve this within GROMACS? Thanks for any advice. Yun -- 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
