Re: [gmx-users] Force constant - units
1 pN/A = 10^-23 kJ/nm2 So 1pN/A = 6,02214129 kJ/mol nm2 Thank you All, Steven On Tue, Jul 3, 2012 at 6:20 PM, Thomas Schlesier wrote: > You have 1mol of your system. > > conversition factor for > kJ/(mol*nm) -> pN is approx 1.661 > > > Am 29.06.2012 10:33, schrieb gmx-users-requ...@gromacs.org: >> >> Dear Gmx Users, >> >> How to recalculate the force constant from the harmonic potential: 1 >> [pN/A] into [kJ/mol nm2] ? Where is the [mol] here? >> >> Thanks, >> >> Steven > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] question about energy minimization
Hi everybody, is there a possibility to define an energy value and when the change of the energy between two steps during the minimization is lower than this value the minimization is finished? Thank you, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Box Borders
Hello, I am running a simulation of a protein-protein complex using explicit solvent. (mdrun -v -deffnm run) I created a box for the simulation (d=5) using editconf: editconf -princ -f conf.gro -bt dodecahedron -d 5.0 -c -o box.gro I am using the option pbc=no in the run.mdp file. Can anyone explain what happens if the complex reaches the "walls" of the box? Does the complex return to the box with the enrgy gained from the collision? Can the complex cross the "walls"? Thanks, Ifat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] BAR gives different result than TI
Hi David, i saw your recent post in the gmx mailing list about "BAR gives different result than TI" i wonder did you get any good answers to this queston so far!? i was also trying to do some free energy calculations, with BAR i seem to get the correct answer (compared to expt and literature) but there still seems to be some issues - see: http://lists.gromacs.org/pipermail/gmx-users/2012-June/072867.html also, i assume you used soft core potentials ... i remember quite a while ago i compared results for free energies of solvation using either sc_power=1 or 2 ... and the results of (as i am sure, converged) calculations differed significantly. but this was a while ago and in the meantime things might have changed. another point: you write that your "numbers seem to have converged pretty good" ... the molecules you use are obviously flexible and i recall talking once to a this guy from some software company, they had done extensive FE calculations and he told me that their main problem was getting converged results for the gas-phase leg of the simulations, in your mail you only gave the net-results for the two molecules, how do the two separate calculations (mutation in vacuum and mutation in solvent) compare? cheers michael === Why be happy when you could be normal? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Modifying Lennard-Jones cross term
Dear GMX users, This is Hyungjun Kim. I try to modify the len= nard jones parameter explicitly. I knew that gromacs provide the com= bination rule such as sigma_12=(sigma_1 + sigma_2 ) /2 like. I fin= d that some specific interaction is quite important, so I want to give expl= icit sigma_12 value for some combination. Could you give me any advi= ce? Thank you in advance. Regards, 김형�= � 드림 --- Hyungjun Kim, Quantum and Computation= al Chemistry Laboratory, Department of Chemistry, KAIST, Daejeon 305= -701, Korea e-mail: [1]hyungjun96= @kaist.ac.kr or [2]jun0906@kai= st.ac.kr phone : 042-350-2861 mobile phone : 010-8537-5051 web : http://qclab.kaist.ac.kr References Visible links 1. file:///tmp/3D"mailto:hyungju...@kaist.ac.kr"; 2. file:///tmp/3D"mailto:jun0...@kaist.ac.kr"; -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Nucleic acid simulation
Hello every one, Im interesting in performing a MD for Protein - RNA complex , Can any one suggest a good tutorial. Thanks in advance. -- Ravi Raja Tejasvi . Merugu http://www.rsquarelabs.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] bindng energy & H bond energy calculation
Thanks Mr.Justin,, I will try them .. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding parameters for pull_groups in mdp file for the pull code
On 7/4/12 2:31 AM, neeru sharma wrote: Dear Gromacs Users, I have some queries about the parameters in the .mdp file for the pull code. If I want to pull my ligand, towards specific atom/group of atoms from the protein, how am I supposed to mentioned these in the mdp file? * pull = umbrella pull_geometry = distance pull_start = yes pull_ngroups= 1 pull_group0 = Ligand pull_group1 = Atom/group of atoms from the protein * Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as "Atoms of the protein". My query is regarding these groups. Shall I just write the name of the Ligand and Atoms (specifying the atom no) or am I supposed to create a separate index file for each of them (one for ligand and other for group of atoms) ? All groups specified in the .mdp file must be either valid default groups or custom groups provided in an index file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nucleic acid simulation
On 7/4/12 6:45 AM, Ravi Raja Merugu wrote: Hello every one, Im interesting in performing a MD for Protein - RNA complex , Can any one suggest a good tutorial. Such systems do not differ significantly from simulations of simple proteins in water, since pdb2gmx can produce topologies for both proteins and nucleic acids. The remaining workflow is basically the same. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Modifying Lennard-Jones cross term
Well, Ill give that a shot from memory of a discussion some time ago, which you could probably track down on the e-mails of past search engine. I think it has to do with force field types, either they list the sigma values, or direct 6, 12 or derived LJ parameters, so it would be related to which force field you use. Otherwise they are in the .rtp, .itp files for specific force fields as tables, and I assume as such you could then put anything you wished in there real or not, as the software would just take the table value. Although I assume someone else has more direct advice, personally though I dont think there would be much of a difference of it unless your atoms pairs have different sigma values than those used in gromacs. You might, if you wished only 2 atoms, have to define an entry for those explicitly, giving some names different from the other things in the .rtp, .itp files, then the respective sigmas in the parameters. The bulletin/email list also has ample things on this (modification of the files) as well, but the files are all strait forward if you just look at them in an editor. Defining the resultant, (example sigma_12) might be hard however, as in either case it still plugs in the parameter to an equation. Otherwise you could plot distances and do the lj calculation by hand, but it might get heck-tick if you include any solvent, or other effects... Good luck Stephan Watkins Original-Nachricht > Datum: Wed, 4 Jul 2012 17:45:56 +0900 (KST) > Von: Hyungjun Kim > An: gmx-users@gromacs.org > Betreff: [gmx-users] Modifying Lennard-Jones cross term >Dear GMX users, > >This is Hyungjun Kim. > >I try to modify the len?ard jones parameter explicitly. > >I knew that gromacs provide the com?ination rule such as >sigma_12=(sigma_1 + sigma_2 ) /2 like. > >I fin? that some specific interaction is quite important, so I want to >give expl?cit sigma_12 value for some combination. > >Could you give me any advi?e? > >Thank you in advance. > >Regards, > >김형??D8 드림 > >--- >Hyungjun Kim, >Quantum and Computation?l Chemistry Laboratory, >Department of Chemistry, KAIST, >Daejeon 305?701, Korea >e-mail: [1]hyungjun96?kaist.ac.kr or [2]jun0906@kai?t.ac.kr > >phone : 042-350-2861 > >mobile phone : 010-8537-5051 > >web : http://qclab.kaist.ac.kr > > References > >Visible links >1. file:///tmp/3D"mailto:hyungju...@kaist.ac.kr"; >2. file:///tmp/3D"mailto:jun0...@kaist.ac.kr"; > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water with atom-based cut-off ...
hi, i'd like to do a simulation of a solute in water - trying to reproduce some literature data i try to be consistent and use an atom-based cut-off. for this each atom needs to be its own charge-group ... so when i change spc.itp from: 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 1 0.41 3 opls_117 1 SOL HW2 1 0.41 to: 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 2 0.41 3 opls_117 1 SOL HW2 3 0.41 grompp complains that for settle all atoms need to be in the same charge group. so i removed the settle and exclusion statements from spc.itp and instead put the commands constraints = h-angles constraint_algorithm = LINCS lincs_order = 8 lincs_iter = 2 in the mdp file ... but now constraints are not applied to waters at all (O and H look as if they move independently) it also didn't help renaming the water molecule, residue and atom names ... any suggestions on how i can apply atom-based cut-off with lincs or shake to water? thanks, michael === Why be happy when you could be normal? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: DNA simulations
Thanks Mark for your response. These are steps I followed to construct DNA+Water molecules. > editconf -f A.pdb -o A.gro -d 0.3 > genbox -cp A.gro -cs -nice -20 -o A_water.gro I have not used any of the topology files (which I believed should be used in g_select) during the construction and I am not sure of handling it. Also, I ned to introduce some OH radicals also into the cylinder with some radius around the DNA. Could you guide me. With regards, Satya. -- View this message in context: http://gromacs.5086.n6.nabble.com/DNA-simulations-tp4998988p4999076.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] DNA simulations
Mark's suggestions were complete. However, you did not follow them. Please follow all of his suggestions and then post back with exactly what you did and exactly what problem you ran into. If you are having trouble with g_select, then show us what you did and why it didn't work. The mailing list should be used in addition to, not as a substitute for, reading the manual and testing it out yourself. Chris. -- original message -- Thanks Mark for your response. These are steps I followed to construct DNA+Water molecules. > editconf -f A.pdb -o A.gro -d 0.3 > genbox -cp A.gro -cs -nice -20 -o A_water.gro I have not used any of the topology files (which I believed should be used in g_select) during the construction and I am not sure of handling it. Also, I ned to introduce some OH radicals also into the cylinder with some radius around the DNA. Could you guide me. With regards, Satya. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Nucleic acid simulation
Heard that RNA/DNA system could be a little trickier than proteins due to the many negative charges. I found somewhen a nice article about RNA simulations in general. Probably some questions you have / will have are answered there: A short guide for molecular dynamics simulations of RNA systems Yaser Hashem, Pascal Auffinger Methods 47 (2009) 187–197 greetings thomas Am 04.07.2012 16:52, schrieb gmx-users-requ...@gromacs.org: On 7/4/12 6:45 AM, Ravi Raja Merugu wrote: > Hello every one, > > Im interesting in performing a MD for Protein - RNA complex , Can any > one suggest a good tutorial. > Such systems do not differ significantly from simulations of simple proteins in water, since pdb2gmx can produce topologies for both proteins and nucleic acids. The remaining workflow is basically the same. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding parameters for pull_groups in mdp file for the pull code
Thanks Justin for your early response. I was confused about it, but now it's clear. Thanks --Neeru > Dear Gromacs Users, > > > I have some queries about the parameters in the .mdp file for the pull code. > > If I want to pull my ligand, towards specific atom/group of atoms from > the protein, how am I supposed to mentioned these in the mdp file? > > * > pull = umbrella > pull_geometry = distance > pull_start = yes > pull_ngroups= 1 > pull_group0 = Ligand > pull_group1 = Atom/group of atoms from the protein > * > > Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as > "Atoms of the protein". My query is regarding these groups. Shall I > just write the name of the Ligand and Atoms (specifying the atom no) > or am I supposed to create a separate index file for each of them (one > for ligand and other for group of atoms) ? > All groups specified in the .mdp file must be either valid default groups or custom groups provided in an index file. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] COM RDF
On 7/4/12 1:07 PM, Dr. Vitaly V. G. Chaban wrote: Dear GROMACS people - I am calculating radial distribution function between the centers of mass of two large particles in a periodic box. My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro My index file contains two groups of atoms standing for the first and the second supraparticles whose centers-of-mass I am interested in. Since here I provide the "conf.gro" file rather than a trajectory, I expect to get just one peak in my RDF, but instead I get multiple peaks at different separation distances (please, see http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index file are separated spatially, if this may matter. Would anyone kindly explain how the COM RDF function works? My ultimate purpose is to depict how the distance between those two centers-of-mass evolves in time. You also need to use the -com flag to use the COM of the reference group. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] COM RDF
>> Dear GROMACS people - >> >> I am calculating radial distribution function between the centers of >> mass of two large particles in a periodic box. >> >> My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f >> conf.gro >> >> My index file contains two groups of atoms standing for the first and >> the second supraparticles whose centers-of-mass I am interested in. >> Since here I provide the "conf.gro" file rather than a trajectory, I >> expect to get just one peak in my RDF, but instead I get multiple >> peaks at different separation distances (please, see >> http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index >> file are separated spatially, if this may matter. >> >> Would anyone kindly explain how the COM RDF function works? My >> ultimate purpose is to depict how the distance between those two >> centers-of-mass evolves in time. >> > > You also need to use the -com flag to use the COM of the reference group. > > -Justin > The -com flag changed the output (please, see http://i48.tinypic.com/29uuo7b.jpg) but there is still a number of embarassing peaks after 7nm. Given the positions of these supraparticles, I would expect maximum about 10nm whereas the box side is 26nm. >From the g_rdf help message -- The option -rdf sets the type of RDF to be computed. Default is for atoms or particles, but one can also select center of mass or geometry of molecules or residues. In all cases, only the atoms in the index groups are taken into account. I understand this in the following way. The centers-of-mass of the groups in the index file are computed and further the calculation proceeds as if these COMs were regular atoms. If I have only two groups, I should get one maximum. Am I not correct? Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] COM RDF
On 7/4/12 1:31 PM, Dr. Vitaly V. G. Chaban wrote: Dear GROMACS people - I am calculating radial distribution function between the centers of mass of two large particles in a periodic box. My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro My index file contains two groups of atoms standing for the first and the second supraparticles whose centers-of-mass I am interested in. Since here I provide the "conf.gro" file rather than a trajectory, I expect to get just one peak in my RDF, but instead I get multiple peaks at different separation distances (please, see http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index file are separated spatially, if this may matter. Would anyone kindly explain how the COM RDF function works? My ultimate purpose is to depict how the distance between those two centers-of-mass evolves in time. You also need to use the -com flag to use the COM of the reference group. -Justin The -com flag changed the output (please, see http://i48.tinypic.com/29uuo7b.jpg) but there is still a number of embarassing peaks after 7nm. Given the positions of these supraparticles, I would expect maximum about 10nm whereas the box side is 26nm. From the g_rdf help message -- The option -rdf sets the type of RDF to be computed. Default is for atoms or particles, but one can also select center of mass or geometry of molecules or residues. In all cases, only the atoms in the index groups are taken into account. I understand this in the following way. The centers-of-mass of the groups in the index file are computed and further the calculation proceeds as if these COMs were regular atoms. If I have only two groups, I should get one maximum. Am I not correct? In theory, yes. I have no idea how effective g_rdf is for this purpose. From your initial description, if you're just trying to track COM distance over time, why not use g_dist? That's precisely what it does. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rms on CA atoms only, with and without mass weighting -nomw
Hi, I'm using gromacs 4.5.4 and I've got a detailed question on how the mass weighting works. Given a trajectory and a pdb from http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.trr I called the following structure="adk_oplsaa.pdb" trajectory="adk_oplsaa.trr" g_rms -s $structure -f $trajectory -o d_rmsd.xvg << EOF 3 3 EOF g_rms -nomw -s $structure -f $trajectory -o d_rmsd_nomw.xvg << EOF 3 3 EOF I was expecting the RMSD values to be identical: all the CA atoms have identical weights with the -mw flag on, which (to my mind) should be yield same results to when -nomw is specified and the same set of atoms is selected. The question: is this an unreasonable expectation? sdiff d_rmsd.xvg d_rmsd_nomw.xvg | tail # consistent only for 5 sig figs 0.0000.369 | 0.0000.368 100.0760.9818456 | 100.0760.9818469 200.1530.8223789 | 200.1530.8223798 300.0000.6450028 | 300.0000.6450034 400.3050.8285408 | 400.3050.8285414 500.3051.9386379 | 500.3051.9386411 600.0001.6888058 | 600.0001.6888076 700.6101.6885630 | 700.6101.6885644 800.6101.8211102 | 800.6101.820 900.6102.1306074 | 900.6102.1306095 (BTW, the g_rms -h mentions something about a '-debug flag' but it seems not to be working.) As a check, I've used MDAnalysis 0.7.6-devel (http://mdanalysis.googlecode.com) and the following code to get RMSD on the same data, which was consistent over 14 sig figs. from MDAnalysis import * from MDAnalysis.analysis.align import * conf = "adk_oplsaa.pdb" traj = "adk_oplsaa.trr" ref = Universe(conf) mob = Universe(conf, traj) rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd.dat", mass_weighted=True) rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd_nomw.dat", mass_weighted=False) sdiff rmsd.dat rmsd_nomw.dat # consistent over 14 sig figs 3.686669177327545608e-04 | 3.686671021799712840e-04 9.818467126090068220e+00 | 9.818467126090039798e+00 8.223796870415890581e+008.223796870415890581e+00 6.450033517100112412e+00 | 6.450033517100091096e+00 8.285414822442923821e+00 | 8.285414822442906058e+00 1.938640271585943964e+01 | 1.938640271585941832e+01 1.688807649241958941e+01 | 1.688807649241956454e+01 1.688564785098214571e+01 | 1.688564785098212795e+01 1.82456215330549e+01 | 1.82456215327706e+01 2.130609827021595137e+01 | 2.130609827021593006e+01 Thanks for helping me figure it out guys, Jan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box Borders
On 4/07/2012 6:17 PM, ifat shub wrote: Hello, I am running a simulation of a protein-protein complex using explicit solvent. (mdrun -v -deffnm run) I created a box for the simulation (d=5) using editconf: editconf -princ -f conf.gro -bt dodecahedron -d 5.0 -c -o box.gro I am using the option pbc=no in the run.mdp file. Can anyone explain what happens if the complex reaches the "walls" of the box? The simulation system is always of infinite extent. You chose for it to be non-periodic. There are no walls in either case. Mark Does the complex return to the box with the enrgy gained from the collision? Can the complex cross the "walls"? Thanks, Ifat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rms on CA atoms only, with and without mass weighting -nomw
On 5/07/2012 10:11 AM, Jan Domanski wrote: Hi, I'm using gromacs 4.5.4 and I've got a detailed question on how the mass weighting works. Given a trajectory and a pdb from http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.trr I called the following structure="adk_oplsaa.pdb" trajectory="adk_oplsaa.trr" g_rms -s $structure -f $trajectory -o d_rmsd.xvg << EOF 3 3 EOF g_rms -nomw -s $structure -f $trajectory -o d_rmsd_nomw.xvg << EOF 3 3 EOF I was expecting the RMSD values to be identical: all the CA atoms have identical weights with the -mw flag on, which (to my mind) should be yield same results to when -nomw is specified and the same set of atoms is selected. The question: is this an unreasonable expectation? sdiff d_rmsd.xvg d_rmsd_nomw.xvg | tail # consistent only for 5 sig figs 0.0000.369 | 0.0000.368 100.0760.9818456 | 100.0760.9818469 200.1530.8223789 | 200.1530.8223798 300.0000.6450028 | 300.0000.6450034 400.3050.8285408 | 400.3050.8285414 500.3051.9386379 | 500.3051.9386411 600.0001.6888058 | 600.0001.6888076 700.6101.6885630 | 700.6101.6885644 800.6101.8211102 | 800.6101.820 900.6102.1306074 | 900.6102.1306095 (BTW, the g_rms -h mentions something about a '-debug flag' but it seems not to be working.) See manual D.1 - the -debug flag takes an argument. As a check, I've used MDAnalysis 0.7.6-devel (http://mdanalysis.googlecode.com) and the following code to get RMSD on the same data, which was consistent over 14 sig figs. from MDAnalysis import * from MDAnalysis.analysis.align import * conf = "adk_oplsaa.pdb" traj = "adk_oplsaa.trr" ref = Universe(conf) mob = Universe(conf, traj) rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd.dat", mass_weighted=True) rms_fit_trj(mob, ref, select="name CA", rmsdfile="rmsd_nomw.dat", mass_weighted=False) sdiff rmsd.dat rmsd_nomw.dat # consistent over 14 sig figs 3.686669177327545608e-04 | 3.686671021799712840e-04 9.818467126090068220e+00 | 9.818467126090039798e+00 8.223796870415890581e+008.223796870415890581e+00 6.450033517100112412e+00 | 6.450033517100091096e+00 8.285414822442923821e+00 | 8.285414822442906058e+00 1.938640271585943964e+01 | 1.938640271585941832e+01 1.688807649241958941e+01 | 1.688807649241956454e+01 1.688564785098214571e+01 | 1.688564785098212795e+01 1.82456215330549e+01 | 1.82456215327706e+01 2.130609827021595137e+01 | 2.130609827021593006e+01 Thanks for helping me figure it out guys, This is expected. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. Mass weighting changes the manner in which round-off error accumulates. Double precision is less affected by this. Your g_rms is single precision, and apparently MDAnalysis is double. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: DNA simulations
On 5/07/2012 12:28 AM, SatyaK wrote: Thanks Mark for your response. These are steps I followed to construct DNA+Water molecules. > editconf -f A.pdb -o A.gro -d 0.3 > genbox -cp A.gro -cs -nice -20 -o A_water.gro That's not going to achieve your objective. I gave you a workflow to do it. You'll need to flesh out the details. I have not used any of the topology files (which I believed should be used in g_select) No, they aren't. during the construction and I am not sure of handling it. Hence the hints I gave about reading documentation... You're doing something very specific and unique to your workflow. GROMACS tries hard to make available tools to solve problems, but there cannot be a one-step shrink-wrap solution for everything you could want to do. Also, I ned to introduce some OH radicals also into the cylinder with some radius around the DNA. Could you guide me. First, find a force field that parameterizes radicals. Good luck with that. ;-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] water with atom-based cut-off ...
On 4/07/2012 11:43 PM, Michael Brunsteiner wrote: hi, i'd like to do a simulation of a solute in water - trying to reproduce some literature data i try to be consistent and use an atom-based cut-off. for this each atom needs to be its own charge-group ... so when i change spc.itp from: 1 opls_116 1SOL OW 1 -0.82 2 opls_117 1SOLHW1 1 0.41 3 opls_117 1SOLHW2 1 0.41 to: 1 opls_116 1SOL OW 1 -0.82 2 opls_117 1SOLHW1 2 0.41 3 opls_117 1SOLHW2 3 0.41 grompp complains that for settle all atoms need to be in the same charge group. so i removed the settle and exclusion statements from spc.itp and instead put the commands Recent versions of spc.itp files include a flexible (ie. non-settle) version that you could be using easily with -DFLEXIBLE see http://www.gromacs.org/Documentation/Include_File_Mechanism. constraints = h-angles constraint_algorithm = LINCS lincs_order= 8 lincs_iter = 2 in the mdp file ... but now constraints are not applied to waters at all (O and H look as if they move independently) h-angles converts bonds to constraints, but there have to be [bonds]. it also didn't help renaming the water molecule, residue and atom names ... any suggestions on how i can apply atom-based cut-off with lincs or shake to water? As you are doing, but better :-) -DFLEXIBLE and h-angles should work well. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Modifying Lennard-Jones cross term
On 4/07/2012 6:45 PM, Hyungjun Kim wrote: >Dear GMX users, > >This is Hyungjun Kim. > >I try to modify the len=ard jones parameter explicitly. > >I knew that gromacs provide the com=ination rule such as >sigma_12=(sigma_1 + sigma_2 ) /2 like. > >I fin= that some specific interaction is quite important, so I want to >give expl=cit sigma_12 value for some combination. > >Could you give me any advi=e? > You can do this, but you will need to have read the parts of chapters 4 and 5 relevant to VDW non-bonded interactions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question about energy minimization
On 4/07/2012 5:46 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, is there a possibility to define an energy value and when the change of the energy between two steps during the minimization is lower than this value the minimization is finished? If it's in manual 7.3.5, you can do it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rms on CA atoms only, with and without mass weighting -nomw
On 07/04/2012 08:34 PM, Mark Abraham wrote: > On 5/07/2012 10:11 AM, Jan Domanski wrote: >> (BTW, the g_rms -h mentions something about a '-debug flag' but it >> seems not to be working.) > > See manual D.1 - the -debug flag takes an argument. > Ah, I see... yes, sorry. > > This is expected. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. Mass > weighting changes the manner in which round-off error accumulates. > Double precision is less affected by this. Your g_rms is single > precision, and apparently MDAnalysis is double. > Alright, thanks! Jan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: DNA simulations
Thanks once again Mark. I am trying to figure out things. Basically, I am using ReaxFF for my simulations. The basic problem I want to address is, to place OH radicals as close as possible to the DNA and rest with water molecules in a box. Thanks, Satya. -- View this message in context: http://gromacs.5086.n6.nabble.com/DNA-simulations-tp4998988p4999093.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: DNA simulations
On 07/05/2012 01:04 PM, SatyaK wrote: Thanks once again Mark. I am trying to figure out things. Basically, I am using ReaxFF for my simulations. Has that been ported to GROMACS? If not, you have that issue to consider first. The basic problem I want to address is, to place OH radicals as close as possible to the DNA and rest with water molecules in a box. The same kind of approach is needed - you need a geometric criterion to split up the waters, etc. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
