[gmx-users] Re: Membrane Simulation
Dear Justin, there were for sure some errors in the command, but even having solved them, the protein still move during the optimization. What I noticed is that the coordinates of the residues seems to decrease to zero and than "restart" from a point out from the box. I mean, taking the first atom of the first residue, after one EM the coordinates were: 1MET N1 6.100 15.879 0.231 after the second EM were 1MET N1 5.469 15.262 0.228 after the third EM were 1MET N1 4.870 14.676 0.225 and so on till the thirteenth EM in which the coordinates were 1MET N1 0.321 10.201 0.207 after this EM, protein moves off the membrane and the coordinates of the first atom of the first residue become: 1MET N1 12.791 9.867 0.206 there is obviously something wrong with the x axis, but what? The box vectors in this case were 6.23910 6.17970 6.91950 and the complete editconf command was "editconf -f protein.gro -o protein_newbox.gro -box 6.23910 6.17970 6.91950 -center 3.20920 2.72175 6.2 -rotate 145 -45 55". I also tried to use a larger box, which vectors were 12 12 12, and in this case the complete editconf command was "editconf -f protein.gro -o proetin.newbox.gro -box 12 12 12 -center 6 6 8.75 -rotate 145 -45 55" and to decrease the scaling factor from 4 to 2, but it was useless. I'm sorry to bother you so much, but I'm stucked with my project. Thank you so much. Yours sincerely, GIuseppe -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Simulation-tp5007421p5007609.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: Membrane Simulation
Dear Justin, thank you very much for replying. When I run the editconf tool I set for sure the right box vectors (6.23910 6.17970 6.91950) so that in the system.gro file (according to the nomenclature of your tutorial) the box vectors from the protein structure and from the membrane are the same, but i noticed that, after using the perl tool, they magically changed (e.g. in the system_inflated.gro file they became 24.95640 24.71880 6.91950). Maybe something is wrong with the "-center" option? I include the complete editconf command that I run: "editconf -f protein_processed.gro -o protein_newbox.gro -c -box 6.23910 6.17970 6.91950 -rotate 85 -10 55 -center 8 8 6". Thanks for your patience and your appreciated help. Yours sincerely, GIuseppe -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Simulation-tp5007421p5007442.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] Membrane Simulation
Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the “-rotate” and “-center” options on, but when I scale the lipid positions with the perl script (before the energy minimization), the protein moves up, de facto off from the membrane! Obviously I've set very strong position-restraining force on protein, but it moves the same. Probably the problem is trivial, but I can't see it, so any help is much appreciated. Thanks a lot, GIuseppe Cimicata -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Simulation-tp5007421.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
Re: [gmx-users] CONSTRAINED SIMULATIONS
Dear Chris: I don't think it is something related to pbc because my solutes are well inside the simulation box (as I told you before I visualize them via a movie while the simulation proceeds). Nor it is something related to the barostat because I saw that warning and in order to try to see it work I decided to do NVT simulations. However, the problem persists. I'm using angle restraints on the "pulled" group in order to preserve its orientation with respect to the reference group. Could this be the problem? Cheers, Giuseppe 2010/1/24 > Dear Giuseppe: > > OK, those are the forces. They seem pretty huge and massively fluctuating, > although I use umbrella sampling myself so this might be quite normal for > constraint sampling (something for you to look into). > > The only thing that comes to mind is that your running up against a pbc > problem in determining either the center of mass of each protein prior to > solving the constraint or that your constraint is oscillating about > different "shortest distances" over different images. > > The gmx3 manual also says this: > > Another limitation is connected with pressure scaling. When pressure > scaling is used, the shortest distance between the pull groups and the > reference group should be within in the central unit-cell, not to periodic > images of the pull groups. Otherwise the pressure scaling will affect the > reference distances and thus also the forces. The exception is constraint > pulling with constraint distance? > 0, this will work correctly with > pressure scaling under all conditions. > > So here's what I recommend: > > 1. create a system that has no water so that it runs faster. > > 2. Use the sd integrator so that you get some random noise. > integrator = sd > tc_grps = System > tau_t = 1.0 > ld_seed = -1 > ref_t = 300 > gen_temp= 300 > gen_vel = yes > unconstrained_start = no > gen_seed= -1 > > 3. see if you can reproduce the problem. > > 4. Make the box much bigger and center your solutes (trjconv -center -pbc > mol) so that you need not worry about pbc problems. > > 5. see if you can reproduce the problem. > > Chris > > -- original message -- > > Got it! > > Ok, first lines: > > # CONSTRAINT3.0 > # Component selection: 1 1 1 > # nSkip 1 > # Ref. Group 'protein_b' > # Nr. of pull groups 1 > # Group 1 'protein_a' Pos. 3.099513 2.982803 3.377482 > # > 0.00-787.501479 > 0.002000-271.159600 > 0.004000-1147.351351 > 0.006000-108.722797 > 0.008000-97.813955 > 0.0158.592018 > 0.012000428.034442 > 0.0140001022.187858 > 0.016000-60.867559 > 0.018000334.483373 > 0.021328.818408 > 0.022000940.307012 > 0.024000368.857413 > 0.0260001680.598490 > 0.028000857.879861 > 0.03362.426529 > 0.0320001717.334105 > 0.034000810.192387 > 0.036000105.655760 > 0.0380001048.031839 > 0.04484.148742 > 0.0420001312.769160 > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CONSTRAINED SIMULATIONS
Got it! Ok, first lines: # CONSTRAINT3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'protein_b' # Nr. of pull groups 1 # Group 1 'protein_a' Pos. 3.099513 2.982803 3.377482 # 0.00-787.501479 0.002000-271.159600 0.004000-1147.351351 0.006000-108.722797 0.008000-97.813955 0.0158.592018 0.012000428.034442 0.0140001022.187858 0.016000-60.867559 0.018000334.483373 0.021328.818408 0.022000940.307012 0.024000368.857413 0.0260001680.598490 0.028000857.879861 0.03362.426529 0.0320001717.334105 0.034000810.192387 0.036000105.655760 0.0380001048.031839 0.04484.148742 0.0420001312.769160 0.044000392.305403 0.046000657.477186 0.0480001044.452911 0.05-529.835976 0.052000-1095.934393 0.054000139.685674 0.05600048.203666 0.058000-414.626373 0.06-1248.120499 0.062000-586.320212 0.064000-1656.690229 0.066000-534.997888 Last lines: 1499.962036 -388.880258 1499.964111 -1041.350388 1499.966064 -4.334934 1499.968018 -143.211905 1499.970093 -471.537546 1499.972046 -869.843672 1499.974121 515.680505 1499.976074 694.682750 1499.978027 856.824896 1499.980103 -675.209433 1499.982056 -617.824015 1499.984131 137.441313 1499.986084 1628.044837 1499.988037 907.738563 1499.990112 604.144941 1499.992065 2013.465537 1499.994019 890.140741 1499.996094 -158.400835 1499.998047 -77.586782 1500.000122 -58.386616 Cheers, Giuseppe 2010/1/24 > Dear Giuseppe: > > *** What I am looking for is raw -pd pull.pdo data from the first run. > *** > > It looks like you did not define a name for -pd: > > mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c > output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 * > > so based on the -h info: > > -pd pull.pdo Output, Opt. Pull data output > > I want to see pull.pdo > > How about the first 100 lines and the last 20 lines. > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CONSTRAINED SIMULATIONS
Chris: you're right man, let me be more concise. Here there is the execution line I used: mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 * As for the pull.ppa file, here you go: ; GENERAL verbose = no Skip steps = 1 ; Runtype: afm, constraint, umbrella runtype = constraint ; Groups to be pulled group_1 = protein_a ; The group for the reaction force. reference_group = protein_b ; Weights for all atoms in each group (default all 1) weights_1= weights_2= weights_3= weights_4= reference_weights= ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com_t0 ; Use running average for reflag steps for com calculation reflag = 1 ; Select components for the pull vector. default: Y Y Y pulldim = Y Y Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r= 1 ; Switch from r to rc in case of dynamic reaction force rc = 1.2 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 1.0 1.0 1.0 ; Rate of chance of the constraint length, in nm/ps ;constraint_rate = 0.0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06 Thank you for your patience. Giuseppe PS: I used the correct files to start the run again and I also visualized the configurations: thus, the pulled protein has moved for real (while it should be stuck at the initial point!). 2010/1/24 > Dear Giuseppe: > > I don't think your method of showing the change is very good since it > introduces unnecessary variables (e.g. did you use the correct files for the > second run). > > What I am looking for is raw -pd pull.pdo data from the first run. I found > no such file in the body of the email and I subscribe to get coallated lists > so I never get email attachments (and wouldn't open them even if I did). > > It looks to me like what you attached is part of mdout.mdp or perhaps -po > pullout.ppa. > > 3.3.3 mdrun -h says: > > -pi pull.ppa Input, Opt. Pull parameters > -popullout.ppa Output, Opt. Pull parameters > -pd pull.pdo Output, Opt. Pull data output > -pn pull.ndx Input, Opt. Index file > > -- original message -- > > Hi Chris, > > the pdo file was attached at the bottom of my previous e-mail. As for > the output, you may read the information about the COMs in the md.log > file. Here there is an extended portion of it at the beginning of the > simulation: > > ** > PULL INFO > ** > RUN TYPE: Constraint > REFERENCE TYPE: center of mass of reference group at t=0 > Looking for group protein_a: found group protein_a: 1323 elements. First: 1 > Looking for group protein_b: found group protein_b: 1323 elements. First: > 1324 > Initializing pull groups. Inv. mass of group 1: 0.70 > Initial coordinates center of mass:3.1002.9833.377 > Initializing reference group. Inv. mass: 0.70 > Initial coordinates center of mass:2.9723.0068.821 > > Constraining the starting coordinates (step -2) > > > And here the same at the beginning of another simulation continuing > from the previous one (duration 1.5 ns): > > ** > PULL INFO > ** > RUN TYPE: Constraint > REFERENCE TYPE: center of mass of reference group at t=0 > Looking for group protein_a: found group protein_a: 1323 elements. First: 1 > Looking for group protein_b: found group protein_b: 1323 elements. First: > 1324 > Initializing pull groups. Inv. mass of group 1: 0.70 > Initial coordinates center of mass:3.0403.6902.740 > Initializing reference group. Inv. mass: 0.70 > Initial coordinates center of mass:2.9763.0058.828 > > Constraining the starting coordinates (step -2). > > > Let me know what you think, thanks. > > Giuseppe > > > 2010/1/24 > > [Hide Quoted Text] > Please provide actual gromacs output and tell us where it is from. I know > it's sad, but not all of us can recall what the gromacs 3.3.3 .pdo file > format looked like. So please include a sufficiently large portion of the > file to help us recall. If, on the other hand, these values that you place > below are from some other tool, then let us know the details a
Re: [gmx-users] CONSTRAINED SIMULATIONS
Hi Chris, the pdo file was attached at the bottom of my previous e-mail. As for the output, you may read the information about the COMs in the md.log file. Here there is an extended portion of it at the beginning of the simulation: ** PULL INFO ** RUN TYPE: Constraint REFERENCE TYPE: center of mass of reference group at t=0 Looking for group protein_a: found group protein_a: 1323 elements. First: 1 Looking for group protein_b: found group protein_b: 1323 elements. First: 1324 Initializing pull groups. Inv. mass of group 1: 0.70 Initial coordinates center of mass:3.1002.9833.377 Initializing reference group. Inv. mass: 0.70 Initial coordinates center of mass:2.9723.0068.821 Constraining the starting coordinates (step -2) And here the same at the beginning of another simulation continuing from the previous one (duration 1.5 ns): ** PULL INFO ** RUN TYPE: Constraint REFERENCE TYPE: center of mass of reference group at t=0 Looking for group protein_a: found group protein_a: 1323 elements. First: 1 Looking for group protein_b: found group protein_b: 1323 elements. First: 1324 Initializing pull groups. Inv. mass of group 1: 0.70 Initial coordinates center of mass:3.0403.6902.740 Initializing reference group. Inv. mass: 0.70 Initial coordinates center of mass:2.9763.0058.828 Constraining the starting coordinates (step -2). Let me know what you think, thanks. Giuseppe 2010/1/24 > Please provide actual gromacs output and tell us where it is from. I know > it's sad, but not all of us can recall what the gromacs 3.3.3 .pdo file > format looked like. So please include a sufficiently large portion of the > file to help us recall. If, on the other hand, these values that you place > below are from some other tool, then let us know the details about that. > > -- original message -- > > Hello, > > I'm trying to do constrained simulations of a system consisting of two > solvated proteins separated at a given distance. Inside the box there are > also > around 14.000 water molecules. At the bottom there is the .pdo > file (I'm using gromacs 3.3.3). > > However, it seems as it does not work. At the beginning of a simulation of > 1.5 ns > this was the positions of the centers of mass of the two proteins: > > Initial coordinates center of mass:3.1002.9833.377 > Initial coordinates center of mass:2.9723.0068.821 > > After 1.5 ns: > > Initial coordinates center of mass:3.0403.6902.740 > Initial coordinates center of mass:2.9763.0058.828 > > The distance changed from 5.445 nm to 6.127 nm. > What's wrong? > > I appreciate your advice on this issue. Thank you very much in advance, > > Joseph > > > ; GENERAL > verbose = no > Skip steps = 1 > ; Runtype: afm, constraint, umbrella > runtype = constraint > ; Groups to be pulled > group_1 = protein_a > ; The group for the reaction force. > reference_group = protein_b > ; Weights for all atoms in each group (default all 1) > weights_1= > weights_2= > weights_3= > weights_4= > reference_weights= > ; Ref. type: com, com_t0, dynamic, dynamic_t0 > reftype = com_t0 > ; Use running average for reflag steps for com calculation > reflag = 1 > ; Select components for the pull vector. default: Y Y Y > pulldim = Y Y Y > ; DYNAMIC REFERENCE GROUP OPTIONS > ; Cylinder radius for dynamic reaction force groups (nm) > r= 1 > ; Switch from r to rc in case of dynamic reaction force > rc = 1.2 > ; Update frequency for dynamic reference groups (steps) > update = 1 > > ; CONSTRAINT RUN OPTIONS > ; Direction, default: 0 0 0, no direction > constraint_direction = 1.0 1.0 1.0 > ; Rate of chance of the constraint length, in nm/ps > ;constraint_rate = 0.0 > ; Tolerance of constraints, in nm > constraint_tolerance = 1e-06 > CONSTRAINED SIMULATIONS > Giuseppe Pellicane giuseppepellicane at gmail.com > Sun Jan 24 11:27:23 CET 2010 > >* Previous message: [gmx-users] simulation crash with GROMOS96 force > field >* Next message: [gmx-users] Re: gas adsorption on CNT >* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > > Hello, > > I'm trying to do constrained simulations of a system c
[gmx-users] CONSTRAINED SIMULATIONS
Hello, I'm trying to do constrained simulations of a system consisting of two solvated proteins separated at a given distance. Inside the box there are also around 14.000 water molecules. At the bottom there is the .pdo file (I'm using gromacs 3.3.3). However, it seems as it does not work. At the beginning of a simulation of 1.5 ns this was the positions of the centers of mass of the two proteins: Initial coordinates center of mass:3.1002.9833.377 Initial coordinates center of mass:2.9723.0068.821 After 1.5 ns: Initial coordinates center of mass:3.0403.6902.740 Initial coordinates center of mass:2.9763.0058.828 The distance changed from 5.445 nm to 6.127 nm. What's wrong? I appreciate your advice on this issue. Thank you very much in advance, Joseph ; GENERAL verbose = no Skip steps = 1 ; Runtype: afm, constraint, umbrella runtype = constraint ; Groups to be pulled group_1 = protein_a ; The group for the reaction force. reference_group = protein_b ; Weights for all atoms in each group (default all 1) weights_1= weights_2= weights_3= weights_4= reference_weights= ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com_t0 ; Use running average for reflag steps for com calculation reflag = 1 ; Select components for the pull vector. default: Y Y Y pulldim = Y Y Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r= 1 ; Switch from r to rc in case of dynamic reaction force rc = 1.2 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 1.0 1.0 1.0 ; Rate of chance of the constraint length, in nm/ps ;constraint_rate = 0.0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
