Re: [gmx-users] Extracting bond information from topol.tpr file using template.c
g_bond.c / gmx_bond.c ? Cheers, Tsjerk On Sep 18, 2012 9:50 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/09/2012 12:49 PM, Amit Shavit wrote: Hello, I'm relatively new to GROMACS, and I need ... The easiest way to learn how to use the information in the .tpr is to work by analogy from an existing tool that has to parse the bonding information, preferably in a similar way. I just can't think of one that really looks at the bonding topology, rather than using a set of atoms belonging to a group, residue or molecule. Why do you want the bonding information? Maybe you don't need it... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u... -- 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] Extracting bond information from topol.tpr file using template.c
On 19/09/2012 4:37 PM, Tsjerk Wassenaar wrote: g_bond.c / gmx_bond.c ? No, I checked earlier and it uses index groups. trjconv -pbc whole is no good either. Mark Cheers, Tsjerk On Sep 18, 2012 9:50 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/09/2012 12:49 PM, Amit Shavit wrote: Hello, I'm relatively new to GROMACS, and I need ... The easiest way to learn how to use the information in the .tpr is to work by analogy from an existing tool that has to parse the bonding information, preferably in a similar way. I just can't think of one that really looks at the bonding topology, rather than using a set of atoms belonging to a group, residue or molecule. Why do you want the bonding information? Maybe you don't need it... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u... -- 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] Extracting bond information from topol.tpr file using template.c
g_hbond does. 19 sep 2012 kl. 05.49 skrev Mark Abraham: On 19/09/2012 12:49 PM, Amit Shavit wrote: Hello, I'm relatively new to GROMACS, and I need to write some of my own analysis tools using the template.c file. I have been able to figure out most of the structure of it, and how the C Structs are used. That is to say, I can successfully retrieve particle positions, residue IDs, residue names, etc. The one piece of information that I can't seem to be able to retrieve is bonding information. Is there a way for me to get this? I should mention that I run the program by inputting a traj.trr and topol.tpr files, so I have access to the information saved in those files. The easiest way to learn how to use the information in the .tpr is to work by analogy from an existing tool that has to parse the bonding information, preferably in a similar way. I just can't think of one that really looks at the bonding topology, rather than using a set of atoms belonging to a group, residue or molecule. Why do you want the bonding information? Maybe you don't need it... 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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] use of PRODRG
On 9/18/12 10:35 PM, Elie M wrote: Dear all, I have been reading about PRODRG that takes a PDB file as an input and produces topologies compatible with GROMACS as an output. Can this program be then considered as a solution to the problem of missing residues in GROMACS like LIG? PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older version produces topologies for the outdated Gromos87), and the quality of the topologies is generally very low. The resulting topologies require significant modification. N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2 version which do not contain the LIG residue appearing in the PDB file. So maybe using PRODRG on the MOL2 might solve the problem? I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Is it possible adding new atomtype to force fields?
On 9/19/12 3:26 AM, Ali Alizadeh wrote: Dear All users Is it possible adding new atomtype to force fields? Yes. Can i prepare a .top file with a combination of input #include and pdb2gmx? Yes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Energy Minimization of Alanin
Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- 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] Energy Minimization of Alanin
On 9/19/12 6:04 AM, Lara Bunte wrote: Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps= 5000 nstlist = 1 rlist= 0.7 coulombtype = PME rcoulomb= 0.7 vdw-type= cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. For EM, the balance of PME vs PP interactions does not matter so much, so you don't necessarily need to take action for this reason. If you are using CHARMM27, however, your cutoffs are completely wrong so you should correct them to have a sensible trajectory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Energy Minimization of Alanin
for EM you can probably ignore this, but note that these are the wrong cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch). On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote: Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] About Energy Minimisation
Dear Mark Thank you for your previous help With your Help I Have successfully Constructed .top and .gro for my cyclic peptide After That i Have solvated and added ions . . But when I do Energy Minimization My Molecule after Energy Minimization ( I have Visualized .gro file in VMD) The bond Between N atom of first Residue ( N-terminal) and C atom of last residue (C-terminal end) Has become Broken . How to Avoid this ? Thanks in Advance -- 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] Residue 'UNK' not found in residue topology database
Dear simone I think so u r using the same pr.mdp and md.mdp files what u created initially. So open both the mdp files replace DRG with UNK and the try sure it will work out. On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/18/12 12:42 PM, SIMONE BROGI wrote: Dear gromacs user, I have a complex generated by docking calculation and I would perform a MD by gromacs. I have a problem with ligand atoms. In the pdb file the ligand appears as UNK and if I process this file in order to start simulation I receive this messagge error: Residue 'UNK' not found in residue topology database this part of file concerning ligand and it is not a residue. In order to fix this problem can I replace the UNK with another tag that is Known in topology database for a ligand??? or How can I fix this error??? Most ligands are not part of existing force fields. Please consult the following: http://www.gromacs.org/**Documentation/Errors#Residue_'** XXX'_not_found_in_residue_**topology_databasehttp://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database http://www.gromacs.org/**Documentation/How-tos/**Parameterizationhttp://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/**Documentation/How-tos/Adding_** a_Residue_to_a_Force_Fieldhttp://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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 -- Regards N.NagaSundaram -- 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] Residue 'UNK' not found in residue topology database
On 9/19/12 8:31 AM, naga sundar wrote: Dear simone I think so u r using the same pr.mdp and md.mdp files what u created initially. So open both the mdp files replace DRG with UNK and the try sure it will work out. The error is from pdb2gmx, so .mdp alterations will have no effect. This error is commonly encountered with a variety of generic residue names (UNK, LIG, DRG, MOL, etc). pdb2gmx is not magic; it has limited support for any non-protein or non-nucleic acid residues. Only a limited number of cofactors and molecules are built into individual force fields, thus leaving the task of parameterization and/or addition of species to a force field to the user. -Justin On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/18/12 12:42 PM, SIMONE BROGI wrote: Dear gromacs user, I have a complex generated by docking calculation and I would perform a MD by gromacs. I have a problem with ligand atoms. In the pdb file the ligand appears as UNK and if I process this file in order to start simulation I receive this messagge error: Residue 'UNK' not found in residue topology database this part of file concerning ligand and it is not a residue. In order to fix this problem can I replace the UNK with another tag that is Known in topology database for a ligand??? or How can I fix this error??? Most ligands are not part of existing force fields. Please consult the following: http://www.gromacs.org/**Documentation/Errors#Residue_'** XXX'_not_found_in_residue_**topology_databasehttp://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database http://www.gromacs.org/**Documentation/How-tos/**Parameterizationhttp://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/**Documentation/How-tos/Adding_** a_Residue_to_a_Force_Fieldhttp://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] How to a .gro file generated from this .top file?
Dear Justin I prepare a .top file with a combination of input #include and pdb2gmx, How can i generate a .gro file from this .top file? Sincerely -- 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] How to a .gro file generated from this .top file?
On 19/09/2012 11:22 PM, Ali Alizadeh wrote: Dear Justin I prepare a .top file with a combination of input #include and pdb2gmx, How can i generate a .gro file from this .top file? You can't - they have radically different kinds of information. Also, see http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. pdb2gmx wrote a coordinate file that matches its .top, which by default will be in .gro format. 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] use of PRODRG
I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? - The LIG residue only appears in the pdb version of the file. I tried to use editconf on the .mol type of file to change into .gro file but it gave an error so I thought editconf only changes pdb files into .gro ones. This raises a question: What other types of files does editconf change into .gro? Anyways, this is a part of the .mol file produced by Marvin Sketch: Mrv0541 09081217542D 46 50 0 0 0 0999 V20005.3375 -1.90290. C 0 0 0 0 0 0 0 0 0 0 0 05.7500 -2.61740. C 0 0 0 0 0 0 0 0 0 0 0 05.1979 -3.23050. S 0 0 0 0 0 0 0 0 0 0 0 04.4443 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 0 4.5305 -2.07440. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -3.3074 0. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -4.54490. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 00.8327 -4.20930. S 0 0 0 0 0 0 0 0 0 0 0 0.. Thanks for your help Elie Date: Wed, 19 Sep 2012 05:23:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] use of PRODRG On 9/18/12 10:35 PM, Elie M wrote: Dear all, I have been reading about PRODRG that takes a PDB file as an input and produces topologies compatible with GROMACS as an output. Can this program be then considered as a solution to the problem of missing residues in GROMACS like LIG? PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older version produces topologies for the outdated Gromos87), and the quality of the topologies is generally very low. The resulting topologies require significant modification. N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2 version which do not contain the LIG residue appearing in the PDB file. So maybe using PRODRG on the MOL2 might solve the problem? I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Ligand-Protein interaction with energy groups
Greetings all, I am trying to compare the stability of two protein-ligand systems where ligands differ. I am trying to observe the difference of interaction energy between the ligands. Would it be correct to make energy groups of Protein, Solvent, Ligand, and compare the energy obtainable by g_energy? I am confused because in one tutorial I do also have to run simulation with only the ligand and solvents. If it were to be correct, would comparing the sum of the LJ-14:Protein-LIG and Coul-14:Protein-LIG of each ligand be okay? Many thanks in advance, John -- 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] Energy Minimization of Alanin
Hi Thanks for the help. I changed this cut-off parameters and increased the distance between my box und the solute from 0.5 to 1.5. I got no error and no note. :-) Greetings Lara - Ursprüngliche Message - Von: Peter C. Lai p...@uab.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 12:12 Mittwoch, 19.September 2012 Betreff: Re: [gmx-users] Energy Minimization of Alanin for EM you can probably ignore this, but note that these are the wrong cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch). On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote: Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Equilibration Water around Alanin - Problem with Names
Hello I want to equilibrate water around the amino acid alanin. I guess I have no further errors up to here. In my pdb file of alanin stands in the first line COMPND Alanin In my topology in the [ moleculetype ] block stands at name: Protein_chain_A. At the end of the topology file stands in the [ system ] block the Name: Alanin in water and in the [ molecules ] block at compund: Protein_chain_A and SOL. In my pr.mdp file for this equilibration I wrote in the output control part energygrps = Protein_chain_A and in the temperature couplin part tc-grps Protein_chain_A SOL The problem is that grompp gives me this error: Fatal error: Group Protein_chain_A not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Does this mean that I have to make an index file first that I should gave to grompp? I don't understand why this error occurs. GROMACS should know Alanin and should know SOL? Thanks for helping me. Lovely Greetings Lara -- 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] Equilibration Water around Alanin - Problem with Names
On 9/19/12 12:27 PM, Lara Bunte wrote: Hello I want to equilibrate water around the amino acid alanin. I guess I have no further errors up to here. In my pdb file of alanin stands in the first line COMPND Alanin In my topology in the [ moleculetype ] block stands at name: Protein_chain_A. At the end of the topology file stands in the [ system ] block the Name: Alanin in water and in the [ molecules ] block at compund: Protein_chain_A and SOL. In my pr.mdp file for this equilibration I wrote in the output control part energygrps = Protein_chain_A and in the temperature couplin part tc-grps Protein_chain_A SOL The problem is that grompp gives me this error: Fatal error: Group Protein_chain_A not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Does this mean that I have to make an index file first that I should gave to grompp? I don't understand why this error occurs. GROMACS should know Alanin and should know SOL? For whatever reason, protein chain names in [molecules] are not recognized by grompp, even though other [moleculetype] names are. What you want is tc-grps = Protein SOL Alanine, by virtue of being a protein residue, will be recognized in the Protein default group. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Theoretical questions about cut-offs and neighbor searching
Hello In my practice calculation I made wrong cut-offs in an energy minimization. After the help of Justin and Peter (thanks a lot) it works and now I have some theoretical question about this. I read about cut-offs in the manual but I don't understand it really. Could you please explain me in a physical meaning what cut-offs are and could you please explain what wrong cut-offs mean for the system? What is the correspondece to neighbor searching, because I always read about neighbor search and don't really understand what is this about. I would be thankful if you use not the same words as in the manual, because I sadly don't understood that :-( (but I will keep trying to understand and read the manual) Thank you Best greetins Lara -- 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] water dynamics
Hi all, I was preparing my system for a simulation and after using grompp i got the following message: Fatal error: Invalid T coupling input: 2 groups, 1 ref_t values and 1 tau_t values For more information and tips for troubleshooting, please check the GROMACS for more information here goes the mdp file: title = 500ps_pr_fixo cpp = /lib/cpp define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 ; total 500 ps comm-mode = Linear nstcomm = 1 nstxout = 500 nstvout = 2 nstfout = 2 nstlog = 1000 nstenergy = 100 nstxtcout = 500 xtc-precision = 1000 energygrps = Protein SOL CL- 3 nstlist = 5 ns_type = grid pbc = xyz rlist = 1.0 domain-decomposition = no coulombtype = PME rcoulomb = 1.0 epsilon-r = 1 vdw-type = Cut-off rvdw = 1.0 DispCorr = EnerPres optimize_fft = yes Tcoupl = V-rescale ;berendsen tc-grps = Protein Non-Protein tau-t = .1 ref-t = 310 gen_vel = yes gen_temp = 310 gen_seed = 173529 Pcoupl = berendsen Pcoupltype = Isotropic tau-p = 1 compressibility = 4.5e-5 ref-p = 1 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no Shake-SOR = no shake-tol = 1e-04 lincs-order = 4 lincs-warnangle = 30 morse = no -- 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] Ligand-Protein interaction with energy groups
On 9/19/12 11:47 AM, 이종화 wrote: Greetings all, I am trying to compare the stability of two protein-ligand systems where ligands differ. I am trying to observe the difference of interaction energy between the ligands. Would it be correct to make energy groups of Protein, Solvent, Ligand, and compare the energy obtainable by g_energy? I am confused because in one tutorial I do also have to run simulation with only the ligand and solvents. You can certainly measure interaction energy in this way, though there are probably more robust methods like LIE and free energy calculations. If it were to be correct, would comparing the sum of the LJ-14:Protein-LIG and Coul-14:Protein-LIG of each ligand be okay? Neither of those terms will be of any use, and should actually be zero. 1-4 interactions are intramolecular. What you're likely more interested in are the LJ-SR and Coul-SR terms, though there are still some flaws with doing that, especially if using PME. This topic is discussed frequently on the mailing list; the archive should provide many useful discussions on such topics. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] use of PRODRG
On 9/19/12 11:40 AM, Elie M wrote: I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? - The LIG residue only appears in the pdb version of the file. I tried to use editconf on the .mol type of file to change into .gro file but it gave an error so I thought editconf only changes pdb files into .gro ones. This raises a question: What other types of files does editconf change into .gro? Anyways, this is a part of the .mol file produced by Marvin Sketch: There is a list (somewhat cryptic if you're not used to reading it) in src/gmxlib/filenm.c, which would suggest a variety of formats are acceptable, but not .mol2 files. Most of the common ones (and some more exotic) can be used: .pdb, .gro, .g96, .g87, .brk, .pqr, .xyz, .ent, .esp, and perhaps a few more, just based on a quick scan. -Justin Mrv0541 09081217542D 46 50 0 0 0 0999 V20005.3375 -1.90290. C 0 0 0 0 0 0 0 0 0 0 0 05.7500 -2.61740. C 0 0 0 0 0 0 0 0 0 0 0 05.1979 -3.23050. S 0 0 0 0 0 0 0 0 0 0 0 04.4443 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 0 4.5305 -2.07440. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -3.3074 0. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -4.54490. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 00.8327 -4.20930. S 0 0 0 0 0 0 0 0 0 0 0 0.. Thanks for your help Elie Date: Wed, 19 Sep 2012 05:23:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] use of PRODRG On 9/18/12 10:35 PM, Elie M wrote: Dear all, I have been reading about PRODRG that takes a PDB file as an input and produces topologies compatible with GROMACS as an output. Can this program be then considered as a solution to the problem of missing residues in GROMACS like LIG? PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older version produces topologies for the outdated Gromos87), and the quality of the topologies is generally very low. The resulting topologies require significant modification. N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2 version which do not contain the LIG residue appearing in the PDB file. So maybe using PRODRG on the MOL2 might solve the problem? I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] use of PRODRG
Thanks for your time and help as usual. Elie Date: Wed, 19 Sep 2012 13:47:26 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] use of PRODRG On 9/19/12 11:40 AM, Elie M wrote: I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? - The LIG residue only appears in the pdb version of the file. I tried to use editconf on the .mol type of file to change into .gro file but it gave an error so I thought editconf only changes pdb files into .gro ones. This raises a question: What other types of files does editconf change into .gro? Anyways, this is a part of the .mol file produced by Marvin Sketch: There is a list (somewhat cryptic if you're not used to reading it) in src/gmxlib/filenm.c, which would suggest a variety of formats are acceptable, but not .mol2 files. Most of the common ones (and some more exotic) can be used: .pdb, .gro, .g96, .g87, .brk, .pqr, .xyz, .ent, .esp, and perhaps a few more, just based on a quick scan. -Justin Mrv0541 09081217542D 46 50 0 0 0 0999 V20005.3375 -1.90290. C 0 0 0 0 0 0 0 0 0 0 0 05.7500 -2.61740. C 0 0 0 0 0 0 0 0 0 0 0 05.1979 -3.23050. S 0 0 0 0 0 0 0 0 0 0 0 04.4443 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 04.5305 -2.07440. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 0 3.7298 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 0 3.0153 -4.54490. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 00.8327 -4.20930. S 0 0 0 0 0 0 0 0 0 0 0 0.. Thanks for your help Elie Date: Wed, 19 Sep 2012 05:23:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] use of PRODRG On 9/18/12 10:35 PM, Elie M wrote: Dear all, I have been reading about PRODRG that takes a PDB file as an input and produces topologies compatible with GROMACS as an output. Can this program be then considered as a solution to the problem of missing residues in GROMACS like LIG? PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older version produces topologies for the outdated Gromos87), and the quality of the topologies is generally very low. The resulting topologies require significant modification. N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2 version which do not contain the LIG residue appearing in the PDB file. So maybe using PRODRG on the MOL2 might solve the problem? I don't understand this. PRODRG will be of no use here since you are using OPLS-AA, and if there is no ligand, then why do you need some external program to build a topology? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
Re: [gmx-users] Theoretical questions about cut-offs and neighbor searching
On 9/19/12 12:54 PM, Lara Bunte wrote: Hello In my practice calculation I made wrong cut-offs in an energy minimization. After the help of Justin and Peter (thanks a lot) it works and now I have some theoretical question about this. I read about cut-offs in the manual but I don't understand it really. Could you please explain me in a physical meaning what cut-offs are and could you please explain what wrong cut-offs mean for the system? What is the correspondece to neighbor searching, because I always read about neighbor search and don't really understand what is this about. I would be thankful if you use not the same words as in the manual, because I sadly don't understood that :-( (but I will keep trying to understand and read the manual) The specifics differ depending on the algorithms used, but in general, the cutoff is the distance beyond which atoms do not contribute to short-range interactions and participate in neighbor lists that are updated every step. Whether or not they contribute to longer-range interactions depends on the algorithms being used (switch and shift for van der Waals, switch, shift, PME, etc for electrostatics). Several molecular simulation textbooks discuss these topics in depth; the manual will not explicitly provide all the necessary information, nor should it. Everything that one needs for better comprehension is cited therein. The main thing for practical purposes is that each force field is validated using a specific set of cutoffs and nonbonded calculation algorithms from which you should not deviate unless you (or others) have proven those settings to be superior to the original derivation. Otherwise, you're using a hacked force field that has no guarantee of producing reliable results. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] water dynamics
On 9/19/12 1:41 PM, Eduardo Oliveira wrote: Hi all, I was preparing my system for a simulation and after using grompp i got the following message: Fatal error: Invalid T coupling input: 2 groups, 1 ref_t values and 1 tau_t values For more information and tips for troubleshooting, please check the GROMACS for more information here goes the mdp file: Tcoupl = V-rescale ;berendsen You have two groups for coupling... tc-grps = Protein Non-Protein and only one set of settings: tau-t= .1 ref-t= 310 Each group controlled by its own thermostat requires its own value of tau_t and ref_t. Two groups = two values. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] distance calculation
Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? -- Tarak -- 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: v-rescale
Dear Sara, I just had a problem with my simulations that I traced to the use of the V-rescale temperature algorithm. Here is my recent post: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121 V-rescale may be appropriate in certain simulations, but it is apparently NOT appropriate when used with Berendsen pressure coupling during the initial equilibration. I don't know if that is related to your problem, but it's something that I just discovered the hard way. -- View this message in context: http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: v-rescale
I am not sure where the idea of using berendsen barostat with the v-rescale thermostat for equilibration came from, however. Doesn't the typical equilibration begin with v-rescale for temperature equilibration then adding parinello-rahman barostat then switching to nose-hoover for production runs (as nose-hoover chains result in the correct canonical distribution)? On 2012-09-19 04:24:27PM -0700, Ladasky wrote: Dear Sara, I just had a problem with my simulations that I traced to the use of the V-rescale temperature algorithm. Here is my recent post: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121 V-rescale may be appropriate in certain simulations, but it is apparently NOT appropriate when used with Berendsen pressure coupling during the initial equilibration. I don't know if that is related to your problem, but it's something that I just discovered the hard way. -- View this message in context: http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Water molecules cannot be settled: V-rescale is the cause
On 9/19/12 5:10 PM, Ladasky wrote: After weeks of trying various conditions, I found my problem. Here, from my position-restrained MDP file, are the two relevant lines: ; Temperature coupling is on tcoupl= V-rescale ; Weak coupling for initial equilibration [snip] ; Pressure coupling is on pcoupl= Berendsen ; Pressure coupling on in NPT, also weak coupling This is a change that I forgot to mention in my list of changes, but in fact I did post the full MDP file. I switched to using two DIFFERENT algorithms for temperature and pressure coupling when I performed the initial position-restrained equilibration. This frequently sets up an INSTABILITY which manifests itself anywhere from a few picoseconds to a full nanosecond into the standard equilibrium MD run. So the initial equilibration was NPT? Did you ever try simply running NVT with either Berendsen or V-rescale before applying any type of pressure coupling? Immediate application of NPT is often unstable for a variety of reasons, not necessarily the temperature coupling algorithm. I am giving this number in real time, rather than in compute cycles, because I tried cutting my step time to 1.0 fs from my usual 2.0 fs -- and I still had a water molecule dislocate abruptly, at nearly the same physical location and simulated time point. I will share my full debugging process if anyone is interested. It took me several runs, all of them over 24 hours long, to figure this out. Now, WHY would I have switched from a Berendsen temperature-coupling algorithm to the V-rescale algorithm? Because of this cautionary note that I started receiving in GROMACS 4.5 when I started the position-restrained mdrun: NOTE 1 [file pr.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I took this as a warning that a deeper study of the algorithms had revealed a flaw in Berendsen, and so I sought to use what GROMACS was advising me would be a better choice. This is apparently MISLEADING advice when doing the initial equilibration. If you are using the Berendsen pressure algorithm, you must also use the Berendsen temperature algorithm. I know that mdrun cannot be sophisticated enough to know which phase of my run I am performing, but I hope that the GROMACS documentation will be revised to discuss the appropriate use of the V-rescale thermostat. I just misused it,and wasted a lot of time as a consequence. I hope that some discussion of its proper use would be written and summarized on a page like, for example, this one: http://www.gromacs.org/Documentation/Terminology/Equilibration It already states: Using, i.e., the Nosé-Hoover thermostat for initial NVT equilibration can lead to wild oscillations of the temperature, with the system ultimately blowing up. A similar warning should be added about the V-rescale thermostat in NPT equilibration, ESPECIALLY if GROMACS is going to issue messages that recommend that you use it! There is a page for the Berendsen barostat/thermostat: http://www.gromacs.org/Documentation/Terminology/Berendsen There is apparently no corresponding page for the V-rescale thermostat. Perhaps one should be written. Anyone is welcome to contribute to the wiki; it is a community project, after all. I would also be interested to see if it can be demonstrated that NPT with V-rescale + Berendsen is unstable after an independent NVT simulation with either method. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Water molecules cannot be settled: V-rescale is the cause
On 20/09/2012 7:10 AM, Ladasky wrote: After weeks of trying various conditions, I found my problem. Here, from my position-restrained MDP file, are the two relevant lines: ; Temperature coupling is on tcoupl= V-rescale ; Weak coupling for initial equilibration [snip] ; Pressure coupling is on pcoupl= Berendsen ; Pressure coupling on in NPT, also weak coupling This is a change that I forgot to mention in my list of changes, but in fact I did post the full MDP file. I switched to using two DIFFERENT algorithms for temperature and pressure coupling when I performed the initial position-restrained equilibration. This frequently sets up an INSTABILITY which manifests itself anywhere from a few picoseconds to a full nanosecond into the standard equilibrium MD run. I am giving this number in real time, rather than in compute cycles, because I tried cutting my step time to 1.0 fs from my usual 2.0 fs -- and I still had a water molecule dislocate abruptly, at nearly the same physical location and simulated time point. This all sounds much like an issue with the topology or starting configuration. As you might know from the advice here http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation, having to use a smaller time step is a routine procedure in case of difficulties. I have seen systems where 0.5 fs without bond constraints was necessary to relax issues with the initial conformation, and using position restraints on (say) all heavy atoms would have made this impossible. Your protocol from July was also asking for trouble by generating velocities and moving straight into an NPT ensemble with position restraints. Starting with an NVT ensemble can be better idea, particularly if the volume is not quite right. I will share my full debugging process if anyone is interested. It took me several runs, all of them over 24 hours long, to figure this out. Now, WHY would I have switched from a Berendsen temperature-coupling algorithm to the V-rescale algorithm? Because of this cautionary note that I started receiving in GROMACS 4.5 when I started the position-restrained mdrun: NOTE 1 [file pr.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I took this as a warning that a deeper study of the algorithms had revealed a flaw in Berendsen, and so I sought to use what GROMACS was advising me would be a better choice. This is apparently MISLEADING advice when doing the initial equilibration. Your observations on one system are not enough to reach this conclusion. v-rescale is normally quite appropriate for equilibration. The above hint is one that only matters when you wish to perform proper equilibrium sampling. Multiple phases of equilibration are normal, particularly in tricky cases, to gradually approach the conditions under which you wish to sample, via those that help deal with trouble with starting conditions. If you are using the Berendsen pressure algorithm, you must also use the Berendsen temperature algorithm. Have you controlled for the fact you were using position restraints before reaching this conclusion? Are the atoms you were restraining in fact in useful locations? Merely switching to the Berendsen temperature algorithm can be lucky enough to lead to stable equilibration. Pathological starting conditions are sometimes quite sensitive. Numerical integration can be a tricky business, and it is difficult to draw general conclusions from limited data. I know that mdrun cannot be sophisticated enough to know which phase of my run I am performing, but I hope that the GROMACS documentation will be revised to discuss the appropriate use of the V-rescale thermostat. I just misused it,and wasted a lot of time as a consequence. I hope that some discussion of its proper use would be written and summarized on a page like, for example, this one: http://www.gromacs.org/Documentation/Terminology/Equilibration It already states: Using, i.e., the Nosé-Hoover thermostat for initial NVT equilibration can lead to wild oscillations of the temperature, with the system ultimately blowing up. A similar warning should be added about the V-rescale thermostat in NPT equilibration, ESPECIALLY if GROMACS is going to issue messages that recommend that you use it! There is a page for the Berendsen barostat/thermostat: http://www.gromacs.org/Documentation/Terminology/Berendsen There is apparently no corresponding page for the V-rescale thermostat. Perhaps one should be written. Most of the documentation of GROMACS is a volunteer effort. I'm sorry you found it inadequate, but I do not think your conclusions are supported by your evidence. Regards, Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] distance calculation
Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/12 2:55 PM, tarak karmakar wrote: Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? g_dist with appropriate index groups. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- Tarak -- 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] distance calculation
On 20/09/2012 2:05 PM, tarak karmakar wrote: Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. g_dist treats the system as a list of atoms, and is ignorant of details like molecules. So you just need to tell it which atoms via their indices. Mark On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/12 2:55 PM, tarak karmakar wrote: Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? g_dist with appropriate index groups. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
