Re: [gmx-users] Parametrisation of the heteroatomic pdb
Justin, I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function? What difference beetwen different caps I cant understand why in my structure there are so non-standart groups. James 2011/11/9 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, Could you tell me another alternative ways to replace existing cap groups in my pdb besides xleap ? ( I've had many problems with the pdb's processed by this soft). Also I've tried to make topology for the non-standart caps by PRODRG but I also have some problems with such parametrisation. Unless you describe your problems, there's very little anyone can or will try to do to help you. I've never had a problem with an xleap coordinate file, so I can't offer you any additional guidance with that. Otherwise, there are dozens of programs that are capable of drawing molecules or editing files. See, for instance: http://www.gromacs.org/**Documentation/File_Formats/** Coordinate_File#Sourceshttp://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Also I've not found suitable topology for some D-isomers ( it's strange that parametriation for such typical non-standart residues is absent in all force fields ). As I understood I cant use topology of L-analogs for the parametrisation of such D-forms because I dont know suitable parameters for dihedrals for instance. Have someone pre-built parameters for the D-aa for Gromos or Charmm force field? Thanks, James 2011/10/29 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, hello! Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ? xleap At this point, please start a new thread for your questions, as these topics are completely unrelated to where you started. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] Parametrisation of the heteroatomic pdb
On 10/11/2011 7:05 PM, James Starlight wrote: Justin, I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function? They can. The purpose of a simulation is to provide a model of reality. How one would wish to cap a peptide depends what is being modelled under what conditions with what objectives in mind. What difference beetwen different caps I cant understand why in my structure there are so non-standart groups. Shrug. We don't even know what they are... Wherever you sourced your starting structure should discuss how and why the termini have such caps. Mark James 2011/11/9 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me another alternative ways to replace existing cap groups in my pdb besides xleap ? ( I've had many problems with the pdb's processed by this soft). Also I've tried to make topology for the non-standart caps by PRODRG but I also have some problems with such parametrisation. Unless you describe your problems, there's very little anyone can or will try to do to help you. I've never had a problem with an xleap coordinate file, so I can't offer you any additional guidance with that. Otherwise, there are dozens of programs that are capable of drawing molecules or editing files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Also I've not found suitable topology for some D-isomers ( it's strange that parametriation for such typical non-standart residues is absent in all force fields ). As I understood I cant use topology of L-analogs for the parametrisation of such D-forms because I dont know suitable parameters for dihedrals for instance. Have someone pre-built parameters for the D-aa for Gromos or Charmm force field? Thanks, James 2011/10/29 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, hello! Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ? xleap At this point, please start a new thread for your questions, as these topics are completely unrelated to where you started. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org
Re: [gmx-users] Normal Mode Analysis
Hi James, PCA on a trajectory is about fluctuations -the correlation between deviations from an average positions-, NMA is about penalized displacement -the increase in potential energy due to concurrent displacement-. In NMA the lowest mode is that for which most atoms can move most unrestrictedly. It seems evident that the side chains will severely penalize the displacement of c-alpha atoms. I wouldn't call that a solvent effect or damping. It's the nature of the protein, and the error you make in your model when restricting to c-alpha atoms only. With respect to the other question, I think the best I can do is to urge you to read more on principal component analysis, until you understand the meaning of 'principal component', 'eigenvalue', 'score', 'projection' and 'loading' :) Cheers, Tsjerk On Thu, Nov 10, 2011 at 8:51 AM, James Starlight jmsstarli...@gmail.com wrote: Hi Tsjerk, Thanks for help. So as I understood if I want to calculate fluctuations only for Calpha I must first to do NMA of my reference in some mode subspace consisted of the eigenvectors for Calpha atoms only. Does this correct ? Previously I've done something like this for random subspace of modes in MMTK (just to reduce the space for calculation) but how perform such operation in Gromacs I havent known yet :) The c-alphas are less hindered in the second model due to the absence of the side chains and such. There's just more freedom. It's known that solevnt for instance could significant damp motions from normal modes. So in my case It seems that sidechains act as the solvent. How do you think may sidechains not only damp motions oberved for C-alpha atoms merely but also change the trajectory of their motion? James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Parametrisation of the heteroatomic pdb
Thanks Mark, 1) By the way do you know any database where I could obtain information about function of the specific CAP groups ? E.g as I know the most spread CAP on N is ACE group but in my case there is For ( simple COH group) instead of ACE. I think that parametrisation of such simple groups should not be very complicate but it's strange that I've not found already built topology for them. 2) Also I've tried to made topology for D amoniacids. I've started with the topology of L analogs e.g for D-val I've created enty based on the Val in .rtp and .hdb files. Not I think I should to invert impropers for the Calpha atoms that new topology represent to true D-isomer :) But I'm not sure about how to make it correctly :) In .itp I've found for new DVA residue [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CA N CCB gi_2 CA CG1 CG2CB gi_2 CCA+N O gi_1 here there are 2 enties for the Ca atoms. What should I do with it for invertion? James 2011/11/10 Mark Abraham mark.abra...@anu.edu.au On 10/11/2011 7:05 PM, James Starlight wrote: Justin, I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function? They can. The purpose of a simulation is to provide a model of reality. How one would wish to cap a peptide depends what is being modelled under what conditions with what objectives in mind. What difference beetwen different caps I cant understand why in my structure there are so non-standart groups. Shrug. We don't even know what they are... Wherever you sourced your starting structure should discuss how and why the termini have such caps. Mark James 2011/11/9 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, Could you tell me another alternative ways to replace existing cap groups in my pdb besides xleap ? ( I've had many problems with the pdb's processed by this soft). Also I've tried to make topology for the non-standart caps by PRODRG but I also have some problems with such parametrisation. Unless you describe your problems, there's very little anyone can or will try to do to help you. I've never had a problem with an xleap coordinate file, so I can't offer you any additional guidance with that. Otherwise, there are dozens of programs that are capable of drawing molecules or editing files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Also I've not found suitable topology for some D-isomers ( it's strange that parametriation for such typical non-standart residues is absent in all force fields ). As I understood I cant use topology of L-analogs for the parametrisation of such D-forms because I dont know suitable parameters for dihedrals for instance. Have someone pre-built parameters for the D-aa for Gromos or Charmm force field? Thanks, James 2011/10/29 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, hello! Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ? xleap At this point, please start a new thread for your questions, as these topics are completely unrelated to where you started. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users
Re: [gmx-users] orca question and LA
Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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] Parametrisation of the heteroatomic pdb
On 10/11/2011 7:36 PM, James Starlight wrote: Thanks Mark, 1) By the way do you know any database where I could obtain information about function of the specific CAP groups ? E.g as I know the most spread CAP on N is ACE group but in my case there is For ( simple COH group) instead of ACE. I think that parametrisation of such simple groups should not be very complicate but it's strange that I've not found already built topology for them. People use acetyl rather than formyl cap either because that's what was used in the experimental system, or because they are simulating a fragment from a larger peptide and acetyl makes for a better model of a peptide bond than formyl for only a small extra cost. I don't even know that any force fields have parameters for H-C(O)-N(H)-R. I suggest you use acetyl. 2) Also I've tried to made topology for D amoniacids. I've started with the topology of L analogs e.g for D-val I've created enty based on the Val in .rtp and .hdb files. Not I think I should to invert impropers for the Calpha atoms that new topology represent to true D-isomer :) But I'm not sure about how to make it correctly :) In .itp I've found for new DVA residue [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CA N CCB gi_2 CA CG1 CG2CB gi_2 CCA+N O gi_1 here there are 2 enties for the Ca atoms. What should I do with it for invertion? First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. Mark James 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 10/11/2011 7:05 PM, James Starlight wrote: Justin, I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function? They can. The purpose of a simulation is to provide a model of reality. How one would wish to cap a peptide depends what is being modelled under what conditions with what objectives in mind. What difference beetwen different caps I cant understand why in my structure there are so non-standart groups. Shrug. We don't even know what they are... Wherever you sourced your starting structure should discuss how and why the termini have such caps. Mark James 2011/11/9 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, Could you tell me another alternative ways to replace existing cap groups in my pdb besides xleap ? ( I've had many problems with the pdb's processed by this soft). Also I've tried to make topology for the non-standart caps by PRODRG but I also have some problems with such parametrisation. Unless you describe your problems, there's very little anyone can or will try to do to help you. I've never had a problem with an xleap coordinate file, so I can't offer you any additional guidance with that. Otherwise, there are dozens of programs that are capable of drawing molecules or editing files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Also I've not found suitable topology for some D-isomers ( it's strange that parametriation for such typical non-standart residues is absent in all force fields ). As I understood I cant use topology of L-analogs for the parametrisation of such D-forms because I dont know suitable parameters for dihedrals for instance. Have someone pre-built parameters for the D-aa for Gromos or Charmm force field? Thanks, James 2011/10/29 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, hello! Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ? xleap At this point, please start a new thread for your questions, as these
Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
Dear Xi Zhao, The ORCAINFO file is no tok. You should not give the Opt keyword there. GMX is taking care of the optimization. If you provide the Opt keyword, ORCA will do an optimization in each QM forces calculation, but neglecting the QM-MM interactions, and this is not what you want. So keep ! RKS B3LYP/G SV(P) TightSCF Opt Hope that helps, Christoph On 11/07/2011 03:45 PM, xi zhao wrote: 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 in addition, how to write ORCAINFO? Is my file right? ! RKS B3LYP/G SV(P) TightSCF Opt or RKS B3LYP/G SV(P) TightSCF Opt --- *11年11月7日，周一, Gerrit Groenhof /ggro...@gwdg.de/* 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午9:23 Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. orca and qm/mm (xi zhao) -- Message: 1 Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST) From: xi zhao zhaoxiitc2...@yahoo.com.cn http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2...@yahoo.com.cn Subject: [gmx-users] orca and qm/mm To: gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Message-ID: 1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com http://cn.mc151.mail.yahoo.com/mc/compose?to=1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com Content-Type: text/plain; charset=utf-8 All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit= 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps= system emtol= 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy= 1 nstxtcout= 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r= 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t= 0.1 0.1 0 ; QM atoms are uncoupled ref_t= 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps= QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp
[gmx-users] Disulphur bridge parameters
Dear gromacs users, I am simulating a protein complex with a disulphur bridge. I put the two chains in the same moleculetype definition, and through pdb2gmx I generate the disulfur bridge. When I checked the .top file for angles and dihedral angles potential parameters I found out that these fields were empty. I wonder why this happens, thanks! Alberto -- 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] Converting of itp topology files
Dear Gromacs Users! I need tto convert topology.itp fule made for my molecule for the old gromos87 force field to the form wich would be suitable for the simulation with the gromos96 force field. What main corrections should I do in my existing .itp topology? Thanks, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CygWin and Gromacs 4.5.5
yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks From: Roland Schulz rol...@utk.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 9, 2011 11:03 AM Subject: Re: [gmx-users] CygWin and Gromacs 4.5.5 On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) . Roland Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] what's the meaning of g_msd's -trestart
dear teacher, i read the groace_manual-4.5.4: i found The time between the reference points for the MSD calculation is set with -trestart. and the defaut is 10ps. do it computer the msd like this : 0ns compared with -beginfit to -endfit 10ns compared with -beginfit to -endfit 20ns compared with -beginfit to -endfit 30ns compared with -beginfit to -endfit thanks!!! Bo Du PHD， Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.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] Running QM/MM in parallel (ORCA/GMX)
Dear Micha, I just saw your mail and perhaps it got already solved in the past. Otherwise: First you should try to set up ORCA calculations in parallel. If that is working, it is relatively straightforward for ORCA/GMX. Simply start GMX one a single CPU, and let ORCA run on several CPUs (by adding the !palX keyword in the ORCAINFO file). Hope that helps, Christoph On 07/11/2011 08:13 PM, Kunze, Micha wrote: Hey there, after working through the helpful tutorials about QM/MM I now ran into a problem when it comes to run ORCA/GROMACS in parallel and I could not find anything about this in the mailing list or on the gromacs page. I can run GROMACS or ORCA in parallel and QM/MM on a single core, but not in parallel using OpenMPI. My machine complains about openmpi as soon as I try to run QM/MM, but it doesn't complain when running a MD simulation in parallel. As a first step, could someone provide an example of how to do a parallel QM/MM run or share some experience? Cheers, Micha - Micha BA Kunze PhD Student Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Steet London, WC1E 6BT UK Mail: micha.kunze...@ucl.ac.uk -- 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] orca question and LA
I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi then make make install are it right? --- 11年11月10日，周四, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午4:47 Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- 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] orca question and LA
I hope you mean ./configure --with-qmmm-orca --without-qmmm-gaussian etc. http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html www.google.com etc. For MPI, I can't really say as I did not get qm/mm with orca/gmx to run in parallel yet (using cp2k atm). Maybe someone else can advise you. Cheers, Micha On 10/11/11 10:49, xi zhao wrote: I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi then make make install are it right? 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *11?11?10?,??, Micha Ben Achim Kunze /ucbt...@live.ucl.ac.uk/* ??: ???: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk ??: Re: [gmx-users] orca question and LA ???: gmx-users@gromacs.org ??: 2011?11?10?,??,??4:47 Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -???- -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Converting of itp topology files
On 10/11/2011 9:30 PM, James Starlight wrote: Dear Gromacs Users! I need tto convert topology.itp fule made for my molecule for the old gromos87 force field to the form wich would be suitable for the simulation with the gromos96 force field. What main corrections should I do in my existing .itp topology? Use pdb2gmx with gromos96 to find out the form of the solution. Then adapt as necessary. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Disulphur bridge parameters
On 10/11/2011 9:28 PM, alberto arrigoni wrote: Dear gromacs users, I am simulating a protein complex with a disulphur bridge. I put the two chains in the same moleculetype definition, pdb2gmx does not read [moleculetype] definitions, it writes them. and through pdb2gmx I generate the disulfur bridge. When I checked the .top file for angles and dihedral angles potential parameters I found out that these fields were empty. I wonder why this happens, thanks! As usual, providing your actual command lines and input would lead to you getting useful help sooner. As it is, I'll guess that you haven't used the specbond.dat mechanism (and/or pdb2gmx -ss option) appropriately. See manual section 5.6.7. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Converting of itp topology files
Mark, The problem is that my .itp done for old gromos ff consist of parameters for molecule wich has some specific groups wich not preset in the gromos96 ff so pdb2gmx is not good decision :) By the way I'm intresting what changes were done in the dihedrail terms since gromos87 ff. E.g I found topology wich consist of parameters for D-amino asids and I want to compare it with L-analogs in gromos96 to find possibe way to make such parametrisation in the gromos96 James 2011/11/10 Mark Abraham mark.abra...@anu.edu.au On 10/11/2011 9:30 PM, James Starlight wrote: Dear Gromacs Users! I need tto convert topology.itp fule made for my molecule for the old gromos87 force field to the form wich would be suitable for the simulation with the gromos96 force field. What main corrections should I do in my existing .itp topology? Use pdb2gmx with gromos96 to find out the form of the solution. Then adapt as necessary. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Converting of itp topology files
On 10/11/2011 10:43 PM, James Starlight wrote: Mark, The problem is that my .itp done for old gromos ff consist of parameters for molecule wich has some specific groups wich not preset in the gromos96 ff so pdb2gmx is not good decision :) Then you'll have to work out how the old .itp worked, and how that functionality works in the current force field and file format. Chapters 4 and 5 are your friends here. Mark By the way I'm intresting what changes were done in the dihedrail terms since gromos87 ff. E.g I found topology wich consist of parameters for D-amino asids and I want to compare it with L-analogs in gromos96 to find possibe way to make such parametrisation in the gromos96 James 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 10/11/2011 9:30 PM, James Starlight wrote: Dear Gromacs Users! I need tto convert topology.itp fule made for my molecule for the old gromos87 force field to the form wich would be suitable for the simulation with the gromos96 force field. What main corrections should I do in my existing .itp topology? Use pdb2gmx with gromos96 to find out the form of the solution. Then adapt as necessary. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Running QM/MM in parallel (ORCA/GMX)
Hey Christoph, I got orca and gmx working in parallel and I already tried it the way you mentioned with gmx on a single cpu and orca with !PALX in the past (with combinations of gmx compiled w/ and w/o mpi enabled), which did not seem to work. I will give it another go! Thanks, Micha On 10/11/11 10:40, Christoph Riplinger wrote: Dear Micha, I just saw your mail and perhaps it got already solved in the past. Otherwise: First you should try to set up ORCA calculations in parallel. If that is working, it is relatively straightforward for ORCA/GMX. Simply start GMX one a single CPU, and let ORCA run on several CPUs (by adding the !palX keyword in the ORCAINFO file). Hope that helps, Christoph On 07/11/2011 08:13 PM, Kunze, Micha wrote: Hey there, after working through the helpful tutorials about QM/MM I now ran into a problem when it comes to run ORCA/GROMACS in parallel and I could not find anything about this in the mailing list or on the gromacs page. I can run GROMACS or ORCA in parallel and QM/MM on a single core, but not in parallel using OpenMPI. My machine complains about openmpi as soon as I try to run QM/MM, but it doesn't complain when running a MD simulation in parallel. As a first step, could someone provide an example of how to do a parallel QM/MM run or share some experience? Cheers, Micha - Micha BA Kunze PhD Student Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Steet London, WC1E 6BT UK Mail: micha.kunze...@ucl.ac.uk -- 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] about the velocity output from leap-frog integrators
On 9/11/2011 9:44 PM, Ravi Bhadauria wrote: Hello users, I have few conflicting answers from the user mailing list about the following question. Using leap-frog integrator, what is the velocity that is WRITTEN in the trajectory file for a frame corresponding to r(t)? Is it v(t-dt/2) or v(t). Has the protocol for writing velocity in trajectory file been consistent from version 3.x to 4.5.x? With leap-frog, it is v(t-dt/2) in 4.5.x. v(t) is never even computed (see do_update_md() in src/mdlib/update.c). I don't know if Erik's statement was accurate in 2002, but it isn't accurate now. Mark Here are few posts hinting its v(t): http://lists.gromacs.org/pipermail/gmx-users/2002-July/001969.html http://lists.gromacs.org/pipermail/gmx-users/2003-September/006956.html Here are couple of posts hinting its v(t-dt/2): http://lists.gromacs.org/pipermail/gmx-users/2006-June/022261.html http://lists.gromacs.org/pipermail/gmx-users/2003-March/004827.html Please let me know. The problem is with certain class of simulations of bounded flows, these two definitions provide contrasting results for suitably averaged velocity. Sincerely Ravi Bhadauria -- 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] Problems with g_membed tools
Hello all, I want to use g_membed to insert a protein in POPC. I followed the manual steps. I used the grompp to generate the tpr file. It works well. But when I handed this tpr file to g_membed, it returned this: --- Program g_membed, VERSION 4.5.3 Source code file: gmx_membed.c, line: 688 Fatal error: Trying to remove more lipid molecules than there are in the membrane --- Why it tries to remove more lipid molecules than there are in the membrane? The membrane has 256 lipid molecules. I used PyMol to see the structure of the protein with POPC. The lipids cover the whole protein. I don't know what's wrong here. Please help me. Thank you! Linda -- 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] what's the meaning of g_msd's -trestart
杜波 wrote: dear teacher, i read the groace_manual-4.5.4: i found The time between the reference points for the MSD calculation is set with -trestart. and the defaut is 10ps. do it computer the msd like this : 0ns compared with -beginfit to -endfit 10ns compared with -beginfit to -endfit 20ns compared with -beginfit to -endfit 30ns compared with -beginfit to -endfit Please consult the following: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problems with g_membed tools
On 11/11/2011 12:05 AM, LindaSong wrote: Hello all, I want to use g_membed to insert a protein in POPC. I followed the manual steps. I used the grompp to generate the tpr file. It works well. But when I handed this tpr file to g_membed, it returned this: --- Program g_membed, VERSION 4.5.3 Source code file: gmx_membed.c, line: 688 Fatal error: Trying to remove more lipid molecules than there are in the membrane --- Why it tries to remove more lipid molecules than there are in the membrane? The membrane has 256 lipid molecules. I used PyMol to see the structure of the protein with POPC. The lipids cover the whole protein. I don't know what's wrong here. We can't know, because you haven't given us information like command lines and output copied from your terminal so we can see the diagnostic information g_membed printed for you. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs/mopac compilation: linking libmopac
Hi all I am trying to compile gromacs with mopac but I'm experience some problems using libmopac.a. I have a x86_64 processor and I'm trying with gromacs-4.5.5. I've followed the instructions at the website (i.e. to compile libmopac.a, I've used the alternte dcart.f and gmxmop.f) but I didn't succeed. I've also seen that this topic have some times appeared in the mailing list but the trick proposed didn't work for me. Here you have the steps with different scenarios I've gone through: **A: Compilation of libmopac.a with fortran compiler then gromacs installation** [ in mopac fortran folder] javier@mopac/fortran/folder $FC -O2 -c *.f(where FC=gfortran or ifort) javier@mopac/fortran/folder ar rcv libmopac.a *.o;ranlib libmopac.a javier@mopac/fortran/folder cp libmopac.a ~/lib/ [in gromacs folder] javier@gromacs/folder ./configure --prefix /home/cerezo/Programas/gromacs-4.5.5_with_mopac/ --with-qmmm-mopac --without-qmmm-gaussian --disable-threads --disable-shared LDFLAGS=-L/home/cerezo/lib CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac javier@gromacs/folder make -j 4 Then I get lots of undefined reference errors: cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -o tpbconv tpbconv.o -L/home/cerezo/lib ./.libs/libgmxpreprocess.a /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd.a ../mdlib/.libs/libmd.a -lfftw3f /home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -ldl -lnsl -lm -lmopac /bin/bash ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -L/home/cerezo/lib -o g_protonate g_protonate.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -lnsl -lm -lmopac /bin/bash ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -L/home/cerezo/lib -o g_luck g_luck.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -lnsl -lm -lmopac /home/cerezo/lib/libmopac.a(gmxmop.o): In function `donhco_': gmxmop.f:(.text+0x23e): undefined reference to `for_f90_index' gmxmop.f:(.text+0x26c): undefined reference to `for_f90_index' gmxmop.f:(.text+0x298): undefined reference to `for_f90_index' ... /home/cerezo/lib/libmopac.a(gmxmop.o): In function `deriv_': gmxmop.f:(.text+0x792): undefined reference to `for_f90_index' gmxmop.f:(.text+0x7c0): undefined reference to `for_f90_index' gmxmop.f:(.text+0x7e1): undefined reference to `for_f90_index' /home/javier/lib/libmopac.a(timer.o)(.text+0x11d): In function `timer_': : undefined reference to `for_write_seq_fmt' ... (an so on for each mopac object) Where I think these refer to internal intel fortran functions (compilation with ifort, analogous errors come with gfortran internal functions). So probably I'm missing something to include this function at gromacs compilation time --- **B: Compilation of libmopac.a with f2c+gcc then gromacs installation** javier@mopac/fortran/folder f2c *.f javier@mopac/fortran/folder gcc -O2 -c *.c javier@mopac/fortran/folder ar rcv libmopac.a *.o;ranlib libmopac.a javier@mopac/fortran/folder cp libmopac.a ~/lib [in gromacs folder] javier@gromacs/folder ./configure --prefix /home/cerezo/Programas/gromacs-4.5.5_with_mopac/ --with-qmmm-mopac --without-qmmm-gaussian --disable-threads --disable-shared LDFLAGS=-L/home/cerezo/lib CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac javier@gromacs/folder make -j 4 This time I also get undefined reference errors, but related to f2c funtions: +timout.c0x105:)(:. textundefined+ 0x3c8reference) :to undefined` do_fioreference' totimer.c :`(do_fio.'text In this case, do I need to include the f2c.h file somewhere in the gromacs qmmm interface code? Could someone point me out where I'm mistaking and what should I do to complete the installation? Thanks Javier -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) -- 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] CygWin and Gromacs 4.5.5
On Tue, Nov 8, 2011 at 11:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Actually I don't think this issue has been addressed. Some NUMA-aware thread_mpi stuff does not work under Cygwin, and code added since 4.5.4 assumes that it does. I can find no reason to support that assumption. To work around, use configure --disable-threads. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity and it would be really much appreciated if people in the future contribute back!!!] Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? That statement was based on my previous experience which, admittedly, might be outdated. I don't remember the exact details, but from what I recall, the I had to fiddle quite a lot with gcc optimizations to get the performance close to MSVC. One detail might be important: the code I was working on is C/C++ mix which quite a lot of ++ in it. Anyway, to get a better picture, it would be nice if people running GROMACS on Windows could share their experience/performance numbers. -- Szilárd Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/**thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/** 2009-September/044792.htmlhttp://cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post
Re: [gmx-users] CygWin and Gromacs 4.5.5
On Thu, Nov 10, 2011 at 5:37 AM, Mr Bernard Ramos bgrquan...@yahoo.comwrote: yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks The slow IO performance under cygwin is a known problem with the approach of cygwin and happens with any cygwin program and cannot be fixed by GROMACS. If you want decent IO performance you need to either use Visual C++ or Msys/MingW (see http://redmine.gromacs.org/issues/448). Roland -- *From:* Roland Schulz rol...@utk.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, November 9, 2011 11:03 AM *Subject:* Re: [gmx-users] CygWin and Gromacs 4.5.5 On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) . Roland Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- 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 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
Re: [gmx-users] Parametrisation of the heteroatomic pdb
Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCG CD1 gd_34 So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ? It could be cool that in that section such information present :) http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral 2011/11/10 Mark Abraham mark.abra...@anu.edu.au First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- 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] Parametrisation of the heteroatomic pdb
On 11/11/2011 3:01 AM, James Starlight wrote: Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCG CD1 gd_34 I've no idea what any of the above was intended to mean. I'll repeat myself again, there's nothing about the improper dihedrals that enforces a particular chirality. Proper dihedrals also don't care about chirality. Chirality is set in the starting configuration, and merely preserved by the force field. So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ? See the #defines in ffbonded.itp. The implementation of the GROMOS force fields are a bit idiosyncratic this way. Mark It could be cool that in that section such information present :) http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- 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] Parametrisation of the heteroatomic pdb
Hi James, I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries. Cheers Tom James Starlight wrote: Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCG CD1 gd_34 So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ? It could be cool that in that section such information present :) http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- Dr Thomas Piggot University of Southampton, UK. -- 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] Parametrisation of the heteroatomic pdb
On 11/11/2011 3:17 AM, Thomas Piggot wrote: Hi James, I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries. Good thought :-) I finally see what my brain was missing - the angle of the improper dihedral is signed, and the relevant square is outside the brackets so the sign matters. The order in which the atoms are specified determines the sign of the angle. So molecules with opposite-sense chiral centres do need different topologies. Mark Cheers Tom James Starlight wrote: Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCG CD1 gd_34 So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ? It could be cool that in that section such information present :) http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- 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: sudden drop of minimal periodic distance
Hi Tsjerk, Thanks for the advice. After I did the nojump conversion of trajectories, there were still quite a few frames with min. dist. under 2.0 nm, but all of them were above 1.4 nm, which I set for rvdw. This is not ideal, but I wonder if it's still OK to use this trajectory? Thanks, Yun Message-ID: cabze1sg24mu7zsh7asvmfainrjsmvgkomg3uy-ixftokwvr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi Yun, Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before using g_mindist. Also visually check a frame that is reported to have closed contacts. Hope it helps, Tsjerk On Nov 10, 2011 1:45 AM, Yun Shi yunsh...@gmail.com wrote: Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm, the min periodic image dist still dropped abruptly to 0.172 or something like this after around 35 ns or 30 ns (different trajectory with same topology). So I wonder if this is just inevitable and we should live with it? Thanks, Yun On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi yunsh...@gmail.com wrote: Hello everyone, I am ... -- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2010/7b9ed4a5/attachment-0001.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: sudden drop of minimal periodic distance
Hi Yun, Well, within 2 nm periodic images can influence each other through ordering of water. But how much that will affect your results and how relevant it is for the properties you're after is hard to tell. I think most people will just continue with analysis, saying that there have been no direct interactions. Cheers, Tsjerk On Nov 10, 2011 6:42 PM, Yun Shi yunsh...@gmail.com wrote: Hi Tsjerk, Thanks for the advice. After I did the nojump conversion of trajectories, there were still quite a few frames with min. dist. under 2.0 nm, but all of them were above 1.4 nm, which I set for rvdw. This is not ideal, but I wonder if it's still OK to use this trajectory? Thanks, Yun Message-ID: cabze1sg24mu7zsh7asvmfainrjsmvgkomg3uy-ixftokwvr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi Yun, Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before using g_mindis... -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2010/7b9ed4a5/attachment-0001.html -- -- 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 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] Parametrisation of the heteroatomic pdb
Thomas, thank you! It's my inattention so I've missed DALA in the rtp file :( So as I've understood the difference just in one string CA N CCB gi_2 for L form CB N CCA gi_2 for D form :D James 2011/11/10 Thomas Piggot t.pig...@soton.ac.uk Hi James, I suggest to see the differences in topologies for L and D amino acids (in the GROMOS force fields at least) you look in the aminoacids.rtp file and in particular the differences between the ALA and DALA entries. Cheers Tom James Starlight wrote: Mark, I've mistaken I need to invert impropers for DIHEDRAL for Calpha atom. By this way I want to change L form to D form for Gromos ff. Does this correct ? [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 NCACBCG gd_34 NCA C+N gd_40 CA CBCG CD1 gd_34 So I think that I need to make corrections in that gd_n files. But in what exactly and where in manual could I read about that parametrisation ? It could be cool that in that section such information present :) http://www.gromacs.org/**Documentation/Terminology/** Dihedral?highlight=dihedralhttp://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral 2011/11/10 Mark Abraham mark.abra...@anu.edu.au mailto: mark.abra...@anu.edu.**au mark.abra...@anu.edu.au First, identify that there's anything to invert. Look at the #define lines for gi_1 and gi_2 and the manual sections for impropers. There's nothing associated with any handedness. The impropers for chirality prevent inversion, rather than enforcing a particular chirality. You can test this yourself. Make a .tpr of an L-amino acid and .gro files of each chirality, and then use mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Problems with g_membed tools
Thank you for reply. I am sorry I didn't apply more information There are only protein and lipids in my system now. I used the CHARMM ff. The topology is like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POPC1 In the grompp step, I used PME to calculate the electrostatic interaction, set the energy group to be Protein and the energy group exclusion to be 'Protein Protein'. I ignored the warning that grompp tells PME not calculating the long-distance interaction,because I think the long-distance interaction does not matter in this membrane insertion (Is this right?). And then get the output tpr file. command line like this: grompp -f membed.mdp -c complex_noLIG_m.pdb -p topol.top -o membed.tpr -maxwarn 1 Then I used the generated tpr file in the g_membed, command line like this: g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000 I selected the Protein to be embeded in and POPC the protein be embeded into; Then the g_membed tells: The estimated area of the protein in the membrane is 11.745 nm^2 There are 1 lipids in the membrane part that overlaps the protein. The area per lipid is inf nm^2. Maximum number of lipids that will be removed is 0. Will resize the protein by a factor of 0.100 in the xy plane and 1.000 in the z direction. This resizing will be done with respect to the geometrical center of all protein atoms that span the membrane region, i.e. z between 2.510 and 7.767 Embedding piece 0 with center of geometry: 5.261230 5.247513 5.138600 --- Program g_membed, VERSION 4.5.3 Source code file: gmx_membed.c, line: 688 Fatal error: Trying to remove more lipid molecules than there are in the membrane For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- So why the maximum number of lipids to be removed is 0? And I don't understand whyin the topology file it says only 1 POPC? This is what I got when I used pdb2gmx to generate the topology file for POPC. Thanks again. Linda -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problems with g_membed tools
On 11/11/11, LindaSong wlsongli...@gmail.com wrote: Thank you for reply. I am sorry I didn't apply more information There are only protein and lipids in my system now. I used the CHARMM ff. The topology is like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POPC1 I thought said you had 256 molecules of lipid... In the grompp step, I used PME to calculate the electrostatic interaction, set the energy group to be Protein and the energy group exclusion to be 'Protein Protein'. I ignored the warning that grompp tells PME not calculating the long-distance interaction,because I think the long-distance interaction does not matter in this membrane insertion (Is this right?). PME does calculate a long-range interaction. From your report, I don't think you are actually using PME, but it is probably irrelevant for membrane insertion. And then get the output tpr file. command line like this: grompp -f membed.mdp -c complex_noLIG_m.pdb -p topol.top -o membed.tpr -maxwarn 1 Use of -maxwarn is a bad habit unless you really know what the problem is and the consequences of ignoring it... Then I used the generated tpr file in the g_membed, command line like this: g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000 I selected the Protein to be embeded in and POPC the protein be embeded into; Then the g_membed tells: The estimated area of the protein in the membrane is 11.745 nm^2 There are 1 lipids in the membrane part that overlaps the protein. The area per lipid is inf nm^2. Maximum number of lipids that will be removed is 0. So there is something catastrophically wrong with the starting configuration... Will resize the protein by a factor of 0.100 in the xy plane and 1.000 in the z direction. This resizing will be done with respect to the geometrical center of all protein atoms that span the membrane region, i.e. z between 2.510 and 7.767 Embedding piece 0 with center of geometry: 5.261230 5.247513 5.138600 --- Program g_membed, VERSION 4.5.3 Source code file: gmx_membed.c, line: 688 Fatal error: Trying to remove more lipid molecules than there are in the membrane For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- So why the maximum number of lipids to be removed is 0? And I don't understand why in the topology file it says only 1 POPC? This is what I got when I used pdb2gmx to generate the topology file for POPC. It's hard to say without knowing what you did with pdb2gmx. You should be able to take your structure file with protein and POPC overlaid, pass that to pdb2gmx and get a correct .top. Depending on how the different POPC molecules are differentiated, you may need to choose pdb2gmx -chainsep differently. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about the velocity output from leap-frog integrators
Thank you for your answer Mark. I was not able to find this information in manual. If it is present, could you please refer me to the relevant section. If it is indeed not there, it would be very helpful to include it in the manual. Sincerely, Ravi Bhadauria On Thu, Nov 10, 2011 at 6:18 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/11/2011 9:44 PM, Ravi Bhadauria wrote: Hello users, I have few conflicting answers from the user mailing list about the following question. Using leap-frog integrator, what is the velocity that is WRITTEN in the trajectory file for a frame corresponding to r(t)? Is it v(t-dt/2) or v(t). Has the protocol for writing velocity in trajectory file been consistent from version 3.x to 4.5.x? With leap-frog, it is v(t-dt/2) in 4.5.x. v(t) is never even computed (see do_update_md() in src/mdlib/update.c). I don't know if Erik's statement was accurate in 2002, but it isn't accurate now. Mark Here are few posts hinting its v(t): http://lists.gromacs.org/pipermail/gmx-users/2002-July/001969.html http://lists.gromacs.org/pipermail/gmx-users/2003-September/006956.html Here are couple of posts hinting its v(t-dt/2): http://lists.gromacs.org/pipermail/gmx-users/2006-June/022261.html http://lists.gromacs.org/pipermail/gmx-users/2003-March/004827.html Please let me know. The problem is with certain class of simulations of bounded flows, these two definitions provide contrasting results for suitably averaged velocity. Sincerely Ravi Bhadauria -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Positive potential energy for TFE solvent
Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? Thanks. Harpreet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problems with g_membed tools
Thank you very much for your reply, Mark It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POPC 256 This problem solved. But then comes a new one. When I did the g_membed, the system blowed up after one iteration! I think I really shouldn't ignore the warning from the grompp. However, as an inexperienced user, I don't know how to improve the mdp file. Can you give me any hint? The mdp file for the g_membed is like this: cpp = /lib/cpp ; Run parameters integrator = md nsteps = 1000 dt = 0.002 ; Output control nstxout = 10 nstvout = 10 nstenergy = 10 nstlog = 10 ; Bond parameters continuation= no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 1 rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = semiisotropic tau_p= 1.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; Energy monitoring energygrps = Protein ; Non-equilibrium MD freezegrps = Protein freezedim = Y Y Y ; Energy group exclusions energygrp_excl = Protein Protein Thanks a lot! Linda -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problems with g_membed tools
On 11/11/2011 5:13 PM, LindaSong wrote: Thank you very much for your reply, Mark It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 POPC 256 This problem solved. But then comes a new one. When I did the g_membed, the system blowed up after one iteration! I think I really shouldn't ignore the warning from the grompp. However, as an inexper ienced user, I don't know how to improve the mdp file. Can you give me any hint? Use a text editor that writes plain text. Junk nbsp; throughout cannot help things. As before, reporting the actual text of the warning is critical to working out what might be wrong. Mark The mdp file for the g_membed is like this: cpp = /lib/cpp ; Run parameters integrator = md nsteps = 1000 dt = 0.002 ; Output control nstxout = 10n bsp; nstvout = 10 nstenergy = 10 nstlog = 10 ; Bond parameters continuation= no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 1 rlist = 1.4 rcoulomb= 1.4 rvdw nb sp; = 1.4 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 nbsp; ref_t = 300 300 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = semiisotropic tau_p= 1.0 compressibility = 4.5e-5 4.5e-5 ref_p ; = 1.0 1.0 ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; Energy monitoring energygrps = Protein ; Non-equilibrium MD freezegrps = Protein freezedim nb sp; = Y Y Y ; Energy group exclusions energygrp_excl = Protein Protein Thanks a lot! Linda -- gmx-users mailing 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] Insertion of the protein into membrane with Gmembed
Dear Gromacs Users! I have some questions about insertion protein into membrane with Gmembed 1) I've used default parameters from gmembed manual for preparing input for insertion integrator = md energygrp = Protein freezegrps = Protein freezedim = Y Y Y energygrp_table energygrp excl = Protein Protein Here Protein is my protein group in topology.top I've obtained 2 warning from gropp WARNING 1 [file gmembed.mdp, line 27]: Unknown left-hand 'energygrp' in parameter file WARNING 2 [file gmembed.mdp, line 27]: Unknown left-hand 'energygrp excl' in parameter file What does it means ? If I ignore those warnings I've obtain No energy groups defined. This is necessary for energy exclusion in the freeze group May be I should define freezegrps as my lipid group not a protein or use ndx file as an alternative ? Thanks, James -- 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: mdp file problem
Dear Justin, I could solve that perticular error but another problem has come, After running energy minimization, the sulphur and mercury(GG)atoms (present in the modified residue of cysteine named CYP at 182 position) break the bonds. On Thu, Nov 10, 2011 at 7:28 PM, madhumita das madhumita.bioi...@gmail.comwrote: Dear Justin, I could resolve that perticular error but another problem has come, After running energy minimization, the sulphur and mercury(GG)atoms (present in the modified residue of cysteine named CYP at 182 position) break the bonds and become freely moving atoms. I have attached my prepared gromacs(aqp_newbox) topology(topol.top) and file obtained after energy mimization(em.gro). Please help me. Madhumita On Tue, Nov 8, 2011 at 5:03 PM, madhumita das madhumita.bioi...@gmail.com wrote: Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , following error comes. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 5000 Step= 17, Dmax= 1.5e-06 nm, Epot= 9.89827e+17 Fmax= inf, atom= 2700 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax 1000. Potential Energy = 9.8982703e+17 Maximum force =inf on atom 2700 Norm of force = 1.7474532e+19 The mdp file is attached. Please help. Madhumita Das -- 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
