[gmx-users] Create a elastic network model -attach a spring between to atoms with force constant
Hi all, I want to create an elastic network model for a protein, in which i have selected only c-alpha atoms(removed rest of the atoms). To attach a spring between alpha atoms with some force(spring) constant k , How can i mention this in topology file ? Thanks, Mohan -- 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] tutorials for Coarse-Grained MD Simulation
For MARTINI force field: http://md.chem.rug.nl/cgmartini/index.php/tutorial Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of J Peterson [think_bey...@aol.com] Sent: Monday, August 06, 2012 6:41 AM To: gmx-users@gromacs.org Subject: [gmx-users] tutorials for Coarse-Grained MD Simulation Dear Gromacs Users, I would like to know if there are any tutorials for Coarse-Grained MD Simulation available anywhere. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Create a elastic network model -attach a spring between to atoms with force constant
On 6/08/2012 5:24 PM, mohan maruthi sena wrote: Hi all, I want to create an elastic network model for a protein, in which i have selected only c-alpha atoms(removed rest of the atoms). To attach a spring between alpha atoms with some force(spring) constant k , How can i mention this in topology file ? In principle, it's not difficult to do this, but you'll need to be well acquainted with various parts of chapters 4 and 5 of the manual, including the example topology files and table 5.5. 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: Adding New Residue to the Gromos 53.6 ff
Mark, The main difficulties is that ATB's output is in the form like [ bonds ] 122 0.1000 1.8700e+07 132 0.1000 1.8700e+07 [ angles ] ; ai aj ak funct angle fc 2132109.50 380.00 2142109.50 425.00 3142109.50 425.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 78 1092 0.00 167.36 8 109 112 0.00 167.36 109 1172 0.00 167.36 etc here I must replace the number of atoms by the corresponded real atoms but also replace the values for the bonds, angles and dihedrals by the Gromacs type codes ( e.g gb_1 etc). This is very routinely for me yet :) I've sent the letter to the ATB's developments with the same proposition to five RTP as the output which could be in some cases more usefull that ITP. James 2012/8/5, Mark Abraham : > On 6/08/2012 4:11 PM, James Starlight wrote: >> Mark, >> >> >> I suppose that the most trivial way to include such external >> topologies is the placement of the ITP file at the bottom of the >> topol.top file ( and addition of two covalent bonds with the adjcent >> residues in case of GFP chromophore ) like in any potein-ligan system. > > No, because bonded interactions can only occur within a [moleculetype]. > >> I think that it must be some script foe convertion itp ro rtp because >> both of that formats have a lot of differenties so the manually >> editing in case of big HET group is very routinely. > > For the ~25 atoms of the GFP chromophore, given a reliable .itp of > Ace-Gly-Cro-Gly-Nme or something, producing an .rtp entry by hand is a > job of up to half an hour, if you understand the .rtp format. > Particularly if the bonded interactions are from the main forcefield, > you've only got to describe atom types, connectivity and charge. > > You could make a feature request of the ATB people for .rtp output > (which might come with supplemental forcefield .itp files). > > Mark > >> >> James >> >> 2012/8/5, Mark Abraham : >>> On 6/08/2012 4:31 AM, James Starlight wrote: Mark, 1) The error was because I've used topology of the CRO generated by the ATB in the ITP form in the RTP file. >>> No, the error "Residue 'CRO' not found in residue topology database" >>> means you haven't put it in the right place, but until you inspect your >>> pdb2gmx output for clues about where it is looking, to help find where >>> you haven't followed the right procedure, you're stuck. You've not told >>> us your command line or shown us any significant output, so you really >>> can't be helped. >>> E.g in RTP file I've found that [ atoms ] is simple C C 0.450 1 when in my ITP its more complicated 7 C1CRO C150.089 12.0110 the main difference is that RTP havent atom order where in IPT file the order of each group is specified. Is there any way to convert ITP back to RTP form ? >>> No. You'll have to do it by hand. >>> 2) I've used specbond.dat to define covalent bonds between C and N termi of chromophore and corresponded termi of the djacent residues ( in GFP chromophore is covalently linked in the midle of the alph helix of that protein in both ends) >>> Sounds like a recipe for trouble, unless you know how to build a >>> two-chain peptide with correct termini into the same [moleculetype], and >>> get specbond.dat to work at the same time. It's possible, but why not >>> use the built in mechanism for head-to-tail peptide linking? >>> >>> Mark >>> James 2012/8/5, Mark Abraham : > James Starlight wrote >> Dear Gromac's users! >> >> I'm working with the GFP protein which has chromophore (CRO) group >> which is covalently bonded to the protein. I want to add new residue >> to the Gromos 53.6 ff. by means of algorithm described here. >> >> >> For that I've coppied files to my local work dirr and modify all of >> them in accordance to the above tutorial- I've coppied .itp of CRO to >> the aminoacids.rtp >> >> [ CRO ] >> [ atoms ] >> etc >> >> I've defined bonds of the djacent real amino acids in the >> specbond.dat > Seems dangerous from my memory of GFP. You should probably be making a > single residue for the whole chromophore, in which case a model that > does > not need specbond.dat is possible. > > > James Starlight wrote >> Finally I've defined CRO (as the protein) in the residuetypes.dat >> >> When I've try use pdb2gmx I've obtain error >> >> Fatal error: >> Residue 'CRO' not found in residue topology database >> >> >> What I've done wrong? >> > If > http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database > and its links don't help, you'll have to inspect carefu
Re: [gmx-users] Re: Adding New Residue to the Gromos 53.6 ff
On 6/08/2012 6:00 PM, James Starlight wrote: Mark, The main difficulties is that ATB's output is in the form like [ bonds ] 122 0.1000 1.8700e+07 132 0.1000 1.8700e+07 [ angles ] ; ai aj ak funct angle fc 2132109.50 380.00 2142109.50 425.00 3142109.50 425.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 78 1092 0.00 167.36 8 109 112 0.00 167.36 109 1172 0.00 167.36 etc here I must replace the number of atoms by the corresponded real atoms but also replace the values for the bonds, angles and dihedrals by the Gromacs type codes ( e.g gb_1 etc). This is very routinely for me yet :) You don't need to replace 122 0.1000 1.8700e+07 with stuff like ConeCtwogb_234 Stuff like ConeCtwo2 0.1000 1.8700e+07 is fine. gb_234 means "paste in the #define in the .itp file"... (seehttp://www.gromacs.org/Documentation/Include_File_Mechanism) so no need to take it out to just paste it in again. See discussion in manual 5.6.1, which of course you've read ;-) Most of what you need to do is to map the atom numbers back to atom names. Most of the rest is doing the +N, -C stuff to use the standard peptide linking machinery. Mark I've sent the letter to the ATB's developments with the same proposition to five RTP as the output which could be in some cases more usefull that ITP. James 2012/8/5, Mark Abraham : On 6/08/2012 4:11 PM, James Starlight wrote: Mark, I suppose that the most trivial way to include such external topologies is the placement of the ITP file at the bottom of the topol.top file ( and addition of two covalent bonds with the adjcent residues in case of GFP chromophore ) like in any potein-ligan system. No, because bonded interactions can only occur within a [moleculetype]. I think that it must be some script foe convertion itp ro rtp because both of that formats have a lot of differenties so the manually editing in case of big HET group is very routinely. For the ~25 atoms of the GFP chromophore, given a reliable .itp of Ace-Gly-Cro-Gly-Nme or something, producing an .rtp entry by hand is a job of up to half an hour, if you understand the .rtp format. Particularly if the bonded interactions are from the main forcefield, you've only got to describe atom types, connectivity and charge. You could make a feature request of the ATB people for .rtp output (which might come with supplemental forcefield .itp files). Mark James 2012/8/5, Mark Abraham : On 6/08/2012 4:31 AM, James Starlight wrote: Mark, 1) The error was because I've used topology of the CRO generated by the ATB in the ITP form in the RTP file. No, the error "Residue 'CRO' not found in residue topology database" means you haven't put it in the right place, but until you inspect your pdb2gmx output for clues about where it is looking, to help find where you haven't followed the right procedure, you're stuck. You've not told us your command line or shown us any significant output, so you really can't be helped. E.g in RTP file I've found that [ atoms ] is simple C C 0.450 1 when in my ITP its more complicated 7 C1CRO C150.089 12.0110 the main difference is that RTP havent atom order where in IPT file the order of each group is specified. Is there any way to convert ITP back to RTP form ? No. You'll have to do it by hand. 2) I've used specbond.dat to define covalent bonds between C and N termi of chromophore and corresponded termi of the djacent residues ( in GFP chromophore is covalently linked in the midle of the alph helix of that protein in both ends) Sounds like a recipe for trouble, unless you know how to build a two-chain peptide with correct termini into the same [moleculetype], and get specbond.dat to work at the same time. It's possible, but why not use the built in mechanism for head-to-tail peptide linking? Mark James 2012/8/5, Mark Abraham : James Starlight wrote Dear Gromac's users! I'm working with the GFP protein which has chromophore (CRO) group which is covalently bonded to the protein. I want to add new residue to the Gromos 53.6 ff. by means of algorithm described here. For that I've coppied files to my local work dirr and modify all of them in accordance to the above tutorial- I've coppied .itp of CRO to the aminoacids.rtp [ CRO ] [ atoms ] etc I've defined bonds of the djacent real amino acids in the specbond.dat Seems dangerous from my memory of GFP. You should probably be making a single residue for the whole chromophore, in which case a model that does not need specbond.dat is possible. James Starlight wrote Finally I've defined CRO (as the protein) in the residuetypes.dat When I've try use pdb2gmx I've obtain error Fatal error: Residue 'CRO' not found in re
[gmx-users] a residue move in extremely large scale in MD
Dear All, I have a protein with about 400 amino acids. I have done a production MD of it. I find in the 400 amino acids, there is 1 amino acids, during the whole MD process, this residue moves in a extremely large scope in comparison with all the other residues. Do you think this single residue with extremely large-scale movement in the whole MD has important biological function, or has no biological function? I am looking forward to getting a reply from you. Cheers, Acoot -- 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] a residue move in extremely large scale in MD
On 6/08/2012 8:58 PM, Acoot Brett wrote: Dear All, I have a protein with about 400 amino acids. I have done a production MD of it. I find in the 400 amino acids, there is 1 amino acids, during the whole MD process, this residue moves in a extremely large scope in comparison with all the other residues. Do you think this single residue with extremely large-scale movement in the whole MD has important biological function, or has no biological function? I'd start by proving that it was not a problem with periodic boundary conditions! If real, movement may or may not be indicative of functional significance - the question is impossible to answer out of context. 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
[gmx-users] Compilation of Gromacs 4.5.5 with GPU support: libxml and CUDA toolkit problems
Hi, I am trying to compile Gromacs 4.5.5 with GPU support on Linux. I have performed the following steps: export OPENMM_ROOT_DIR=/home//gromacs/OpenMM2.0-Linux64/ mkdir build-gpu mkdir exec-gpu cd build-gpu cmake ../ -DGMX_OPENMM=ON -DFFTW3F_INCLUDE_DIR=/usr/lib/include -DFFTW3F_LIBRARIES=/usr/lib/libfftw3f.a -DCMAKE_INSTALL_PREFIX=../exec-gpu -DGMX_X11=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX="_gpu" -DGMX_LIBS_SUFFIX="_gpu" -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DLIBXML_INCLUDE_DIR=/usr/lib but it fails with: -- Using manually set binary suffix: "_gpu" -- Using manually set library suffix: "_gpu" -- checking for module 'libxml-2.0' -- package 'libxml-2.0' not found -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR) CMake Error at cmake/FindCUDA.cmake:465 (message): Specify CUDA_TOOLKIT_ROOT_DIR Call Stack (most recent call first): CMakeLists.txt:434 (find_package) For libxml2: I have libxml2.so.2 in /usr/lib I tried the following: - export LIBXML2_INCLUDE_DIR=/usr/lib - export LIBXML2_LIBRARIES=/usr/lib/libxml2.so.2 - adding -DLIBXML2_INCLUDE_DIR=/usr/lib but it continues to fail. About the CUDA_TOOLKIT_ROOT_DIR, I don't know where to find it honestly. Any hint on how to find a solution? Thanks a lot, Massimo -- Massimo Sandal, Ph.D. http://devicerandom.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] Hydroxyapatite MD odd behavior
Justin, Of course you are right, for troubleshooting the smaller, the better. However, in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell, the later is by no means small. In response to your comments, I will appreciate very much if you could examine the PDB files related to the HAP geometry. They can be downloaded from http://www.fis.unam.mx/~ramon/CursoDF/HAP/ They are named hap-2 and slab-2, the first one corresponds to the unit cell from which we built the slab (which is labed slab-2) upon which we want to study the peptide interactions. The *.itp file I sent before corresponds to hap-2. We hope that with this information you can help us in detecting the source of the problem that has bother us for some time now... Sorry for the delay in responding but I had problems sending the pdb files through gmx-users... Cheers, On Fri, 27 Jul 2012 22:29:31 -0400, Justin Lemkul wrote > On 7/27/12 8:54 PM, Ramon Garduno wrote: > > Dear Justin, > > > > Thanks for your quick reply. Actually, we think that the topology is OK, > > however HAP's parameters could be wrong, we are checking on this... > > > > I would say that the topology being OK and the parameters being > wrong are contradictory statements ;) > > > These are the topology files used for HAP. The names associated to the atoms > > present on the slab are: > > > > Can you reduce the system to just one molecule? It appears there > are several molecules in the .itp below and it's quite hard to keep > track of everything without seeing the corresponding coordinate file > as well. A single molecule would be a lot easier to deal with, and > a coordinate file would allow for better troubleshooting (the > smaller, the better). > > -Justin > > > ACa - Ca2+ > > AP - P > > AO1 - O(P) > > AO4 - O(H) > > AH - H > > > > 1- ffnonbonded.itp > > [ atomtypes ] > > ;name at.num mass charge ptype c6 c12 > >ACa 40.0800 0.000 A 7.34375e-05 4.755341e-08 > > AP 30.9738 0.000 A 1.6701174e-03 2.9953696e-06 > >AO1 15.9994 0.000 A 1.8737825e-04 1.4573462e-07 > >AO4 15.9994 0.000 A 9.793663e-05 8.5730467e-08 > > AH 1.00800 0.000 A 7.17e-11 5.497e-16 > > > > [ nonbond_params ] > > ; i j func c6 c12 > > ACa ACa 1 7.34375e-05 4.755341e-08 > > ACa AO4 1 8.480696e-05 6.38496e-08 > > ACa AH 1 7.2564e-085.112734e-12 > > ACa AO1 1 1.173055e-04 8.324769e-08 > > ACa AP 1 3.50213e-04 3.77223e-07 > > AO4 AO4 1 1.8737825e-04 8.5730467e-08 > > AO4 AH 1 8.37977e-08 6.864841e-12 > > AO4 AO1 1 1.354666e-04 1.117761e-07 > > AO4 AP 1 1.2789279e-03 5.0674888e-07 > >AH AH 1 7.17e-11 5.497e-16 > >AH AO1 1 1.159095e-07 8.950437e-12 > >AH AP 1 3.460454e-07 4.057776e-11 > > AO1 AO1 1 1.8737825e-04 1.4573462e-07 > > AO1 AP 1 5.594137e-04 6.607035e-07 > >AP AP 1 1.6701174e-03 2.9953696e-06 > > > > 2- HAP-MODEL4-100.itp > > ;; topology file for a HAP, created by Eduardo Villarreal & Ramon Garduno > > ;; from hap.itp taken from diferente papers > > ;; one can use Gromacs force-field files (ffgmx*.itp) > > ;; If you use this topology file, please cite to Eduardo Villarreal & Ramon > > Garduno > > ;; > > > > [ moleculetype ] > > ; Name nrexcl > > HAP 3 > > > > [ atoms ] > > ;aqui se hace coincidir cada atomo en la celda de unidad > > ; idatype resnr resaneaname cgnrcharge mass > > 1 AO1 1HAP O3A 1-1.4000 15.9994 > > 2 AO1 1HAP O3B 2-1.4000 15.9994 > > 3 AO1 1HAP O3C 3-1.4000 15.9994 > > 4 AO1 1HAP O3D 4-1.4000 15.9994 > > 5 AO1 1HAP O3E 5-1.4000 15.9994 > > 6 AO1 1HAP O3F 6-1.4000 15.9994 > > 7 AO1 1HAP O3G 7-1.4000 15.9994 > > 8 AO1 1HAP O3H 8-1.4000 15.9994 > > 9 AO1 1HAP O3I 9-1.4000 15.9994 > > 10 AO1 1HAP O3J 10-1.4000 15.9994 > > 11 AO1 1HAP O3K 11-1.4000 15.9994 > > 12 AO1 1HAP O3L 12-1.4000 15.9994 > > 13 AO1 1HAP O3M 7-1.4000 15.9994 > > 14 AO1 1HAP O3N 8-1.4000 15.9994 > > 15 AO1 1HAP O3O 9-1.4000 15.9994 > > 16 AO1 1HAP O3P 10-1.4000 15.9994 > > 17 AO1 1HAP O3Q 11
[gmx-users] Re: How to add new residue(LIG reisdue)? (Justin Lemkul)
Please keep all Gromacs-related correspondence on the gmx-users mailing list. On 8/6/12 1:47 PM, Ali Alizadeh wrote: Dear Justin I Know your reply. But, All my pdb file for each molecules contain LIG residue. What's LIG residue? Why LIG residue exists in any pdb files, I used avogadro software, Please help me, i study normal alkanes behavior by means of molecular dynamic, Only you know what "LIG" means. That's probably just some generic designator for a ligand or small molecule. -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] Hydroxyapatite MD odd behavior
On 8/6/12 1:35 PM, Ramon Garduno wrote: Justin, Of course you are right, for troubleshooting the smaller, the better. However, in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell, the later is by no means small. In response to your comments, I will appreciate very much if you could examine the PDB files related to the HAP geometry. They can be downloaded from http://www.fis.unam.mx/~ramon/CursoDF/HAP/ They are named hap-2 and slab-2, the first one corresponds to the unit cell from which we built the slab (which is labed slab-2) upon which we want to study the peptide interactions. The *.itp file I sent before corresponds to hap-2. We hope that with this information you can help us in detecting the source of the problem that has bother us for some time now... Please provide all the necessary files, including topologies and modified force field files. I don't have time to make and double-check all of these files and it's better to use exactly the same files you've been trying to use. Sorry for the delay in responding but I had problems sending the pdb files through gmx-users... Attachments are no longer allowed due to recent viruses and spam. Posting files for download from external sites is the only way to provide files (aside from copying and pasting their contents, but external download is probably easiest in many cases). -Justin Cheers, On Fri, 27 Jul 2012 22:29:31 -0400, Justin Lemkul wrote On 7/27/12 8:54 PM, Ramon Garduno wrote: Dear Justin, Thanks for your quick reply. Actually, we think that the topology is OK, however HAP's parameters could be wrong, we are checking on this... I would say that the topology being OK and the parameters being wrong are contradictory statements ;) These are the topology files used for HAP. The names associated to the atoms present on the slab are: Can you reduce the system to just one molecule? It appears there are several molecules in the .itp below and it's quite hard to keep track of everything without seeing the corresponding coordinate file as well. A single molecule would be a lot easier to deal with, and a coordinate file would allow for better troubleshooting (the smaller, the better). -Justin ACa - Ca2+ AP - P AO1 - O(P) AO4 - O(H) AH - H 1- ffnonbonded.itp [ atomtypes ] ;name at.num mass charge ptype c6 c12 ACa 40.0800 0.000 A 7.34375e-05 4.755341e-08 AP 30.9738 0.000 A 1.6701174e-03 2.9953696e-06 AO1 15.9994 0.000 A 1.8737825e-04 1.4573462e-07 AO4 15.9994 0.000 A 9.793663e-05 8.5730467e-08 AH 1.00800 0.000 A 7.17e-11 5.497e-16 [ nonbond_params ] ; i j func c6 c12 ACa ACa 1 7.34375e-05 4.755341e-08 ACa AO4 1 8.480696e-05 6.38496e-08 ACa AH 1 7.2564e-085.112734e-12 ACa AO1 1 1.173055e-04 8.324769e-08 ACa AP 1 3.50213e-04 3.77223e-07 AO4 AO4 1 1.8737825e-04 8.5730467e-08 AO4 AH 1 8.37977e-08 6.864841e-12 AO4 AO1 1 1.354666e-04 1.117761e-07 AO4 AP 1 1.2789279e-03 5.0674888e-07 AH AH 1 7.17e-11 5.497e-16 AH AO1 1 1.159095e-07 8.950437e-12 AH AP 1 3.460454e-07 4.057776e-11 AO1 AO1 1 1.8737825e-04 1.4573462e-07 AO1 AP 1 5.594137e-04 6.607035e-07 AP AP 1 1.6701174e-03 2.9953696e-06 2- HAP-MODEL4-100.itp ;; topology file for a HAP, created by Eduardo Villarreal & Ramon Garduno ;; from hap.itp taken from diferente papers ;; one can use Gromacs force-field files (ffgmx*.itp) ;; If you use this topology file, please cite to Eduardo Villarreal & Ramon Garduno ;; [ moleculetype ] ; Name nrexcl HAP 3 [ atoms ] ;aqui se hace coincidir cada atomo en la celda de unidad ; idatype resnr resaneaname cgnrcharge mass 1 AO1 1HAP O3A 1-1.4000 15.9994 2 AO1 1HAP O3B 2-1.4000 15.9994 3 AO1 1HAP O3C 3-1.4000 15.9994 4 AO1 1HAP O3D 4-1.4000 15.9994 5 AO1 1HAP O3E 5-1.4000 15.9994 6 AO1 1HAP O3F 6-1.4000 15.9994 7 AO1 1HAP O3G 7-1.4000 15.9994 8 AO1 1HAP O3H 8-1.4000 15.9994 9 AO1 1HAP O3I 9-1.4000 15.9994 10 AO1 1HAP O3J 10-1.4000 15.9994 11 AO1 1HAP O3K 11-1.4000 15.9994 12 AO1 1HAP O3L 12-1.4000 15.9994 13 AO1 1HAP O3M 7-1.4000 15.9994
Re: [gmx-users] Hydroxyapatite MD odd behavior
On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote > Please provide all the necessary files, including topologies and > modified force field files. I don't have time to make and double- > check all of these files and it's better to use exactly the same > files you've been trying to use. > Dear Justin, Thank you for your prompt response and willingness to help us... Since we do not have problems with the protein-water system, we decided to look closely to what happens with the slab during the NVT simulation. Thus, I have placed in http://www.fis.unam.mx/~ramon/CursoDF/HAP/ for download all the files we are using (at your request) to analyze the extrange behavior observed on the tetrahedral phosphate ion. Hopefuly your trained eyes can see what we can not... Cheers, Ramon Garduno UNAM, Instituto de Ciencias Fisicas Cuernavaca, Mexico -- Open WebMail Project (http://openwebmail.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] Hydroxyapatite MD odd behavior
On 8/6/12 3:13 PM, Ramon Garduno wrote: On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote Please provide all the necessary files, including topologies and modified force field files. I don't have time to make and double- check all of these files and it's better to use exactly the same files you've been trying to use. Dear Justin, Thank you for your prompt response and willingness to help us... Since we do not have problems with the protein-water system, we decided to look closely to what happens with the slab during the NVT simulation. Thus, I have placed in http://www.fis.unam.mx/~ramon/CursoDF/HAP/ for download all the files we are using (at your request) to analyze the extrange behavior observed on the tetrahedral phosphate ion. Hopefuly your trained eyes can see what we can not... Immediately there is a problem. Your cutoff values in the .mdp files (which are incorrect for Gromos96 53A6) are larger than the size of the small system will permit, causing grompp to fail with a fatal error. If you're overriding this error with -maxwarn, then you're trying to simulate an unreasonable system since it violates the minimum image convention. If you're working with other systems that are larger or different, please provide those files instead. I've already had to make a large number of corrections to these files (mostly in atom naming/capitalization) to get grompp to even run, so parsing out those errors is somewhat annoying. -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] NMA and g_nmeig segmentation fault
Hello All -- I'm trying to do a normal modes analysis of a fairly large crystal system (~20,000 atoms) in double-precision GROMACS. The system is xy periodic with 2 9-3 walls, and has periodic molecules. I first minimized the structure with L-BFGS to 1e-5 tolerance with switched vdW interactions and PME electrostatics (3dc geometry). When I tried to run g_nmeig on the matrix, I received the following error message from the shell /var/spool/pbs/mom_priv/jobs/2480011.lionxj.rcc.psu.edu.SC: line 7: 3205 Segmentation fault g_nmeig_d -f wall3_nm -s wall3_nm -T 300 -first 1 -last 2 -of wall3_efreq -ol wall3_eigval -v wall3_eigvec >&nm.g_nmeig The last thing written to the g_nmeig output is Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision) Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.5.5 I was able to successfully run NMA using the same code on a similar system that was only 1/3 of the current size (reaction-field-zero electrostatics) and also on a system 1/3 of the size with xyz periodicity and PME electrostatics, and received no segmentation fault error. I'm a little bit baffled about the source of the segmentation error, because I would have expected it to crash during the Hessian calculation if there were a problem with allocating system memory or essentially singular forces. Has anyone else encountered a similar problem? Thanks in advance for your help. -- Mike Howard -- 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] NMA and g_nmeig segmentation fault
On 7/08/2012 7:07 AM, Michael Howard wrote: Hello All -- I'm trying to do a normal modes analysis of a fairly large crystal system (~20,000 atoms) in double-precision GROMACS. The system is xy periodic with 2 9-3 walls, and has periodic molecules. I first minimized the structure with L-BFGS to 1e-5 tolerance with switched vdW interactions and PME electrostatics (3dc geometry). When I tried to run g_nmeig on the matrix, I received the following error message from the shell /var/spool/pbs/mom_priv/jobs/2480011.lionxj.rcc.psu.edu.SC: line 7: 3205 Segmentation fault g_nmeig_d -f wall3_nm -s wall3_nm -T 300 -first 1 -last 2 -of wall3_efreq -ol wall3_eigval -v wall3_eigvec &nm.g_nmeig The last thing written to the g_nmeig output is Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision) Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.5.5 I was able to successfully run NMA using the same code on a similar system that was only 1/3 of the current size (reaction-field-zero electrostatics) and also on a system 1/3 of the size with xyz periodicity and PME electrostatics, and received no segmentation fault error. I'm a little bit baffled about the source of the segmentation error, because I would have expected it to crash during the Hessian calculation if there were a problem with allocating system memory or essentially singular forces. Has anyone else encountered a similar problem? Diagonalizing the Hessian requires memory proportional to N^2, so your symptoms seem consistent with not having enough memory for the job. You can probably probe for this by using only part of the system, or single precision, more virtual memory, or a bigger machine. 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
[gmx-users] RE: tutorials for Coarse-Grained MD Simulation
Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the available Martini files and programs with the recent version of GROMACS that is version 4? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p486.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
