Re: [gmx-users] Re: Justin lipid-position restraine
On Tue, May 8, 2012 at 1:01 PM, rama david ramadavidgr...@gmail.com wrote: On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs user, I am doing the justin tutorial on lipid posted on link.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I am following the tutorial very carefully ... As mentioned in the tutorial I need to generate strong position restrained on proteins heavy atoms to ensure that position of atom does not change during EM (Energy Minimisation ) My command line is as follow . genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Reading structure file Select group to position restrain Group 0 ( System) has 138 elements Group 1 (Protein) has 138 elements Group 2 ( Protein-H) has 109 elements Group 3 (C-alpha) has16 elements Group 4 ( Backbone) has48 elements Group 5 ( MainChain) has64 elements Group 6 ( MainChain+Cb) has78 elements Group 7 (MainChain+H) has81 elements Group 8 ( SideChain) has57 elements Group 9 (SideChain-H) has45 elements Select a group: I am using Gromacs 4.5.4 Generally position restrain is applied on backbone of protein So I choose backbone (4) Is it right or I have to choose the group protein(138 elements) to apply position restraine on all protein atoms As the tutorial suggest you can restrain the heavy atoms, but I usually restrain the entire protein during the InflateGro steps (EMs) and let the lipids minimize around it. -Anirban All suggestions are welcome thank you in advance Rama David . -- 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] itp file problem
On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran bskumar.t...@gmail.com wrote: First i had simulation of the protein alone in united atom gromacs force field by -ff gmx in pdb2gmx now i am unable to run the protein-ligand complex for the same protein with a ligand, it says the following error due to itp file generated from PRODRG, if i change the force field its says atom mismatch. Please help me Change the force-field means? Did you change the FF with pdb2gmx, or just in your .top file? What is the way to run the simulation grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c prt_b4ion.pdb InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -pprt.top InputTopology file -pp processed.top Output, Opt. Topology file -o prt_b4ion.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp Generated 1284 of the 1485 non-bonded parameter combinations Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp --- Program grompp-4.0.7, VERSION 4.0.7 Source code file: toppush.c, line: 947 Fatal error: Atomtype CR1 not found --- I Caught It In the Face (P.J. Harvey) Did you include the ligand's itp file in your .top file? I think you haven't. [ grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp-4.0.7 (-: Option Filename Type Description
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Mon, May 7, 2012 at 10:17 AM, Bala S think_bey...@aol.com wrote: Justin and Anirban, I have another query on membrane simulation following your tutorials. How do I insert only a part of protein into the lipid bilayer and carryout the simulation? editconf with -box option helps you to orient your protein with respect to the bilayer. And visually in VMD you have the option of move a molecule under mouse option in which you can move your protein wrt the bilayer (when the bilayer and the protein .gro/.pdb files are loaded separately in VMD). -Anirban Thanks Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4957017.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] membrane simulation
On Thu, May 3, 2012 at 4:38 PM, scapr...@uniroma3.it wrote: Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the KALP15 in DPPCI Tutorial and, so far, I managed to obtain my protein (in pdb code) very close to the membrane surface by using editconf and cat command. At this point, I don't know how to get on. 1)How should I generate the topology file which includes the coordinates both of the protein and of the membrane? If you are using the ff53a6 FF then you need to add the appropriate lipid parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files which is very well explained in the tutorial. Then in your .top file you need to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can directly use pdb2gmx on your system (I suppose DPPC is already included in it). If you wish to use the ff43a1 FF, then you can find the modified .itp files at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial . 2)Furthermore, the lipid molecules are listed in my pdb file with the abbreviation DPP, whereas I see that those ones are called DPPC in the Tutorial. Therefore, Should I replace DPP abbreviation with DPPC in my pdb file? Could this difference cause any bugs in the next steps? PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file. -Anirban Any suggestion would be appreciated, Silvia -- 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] jointly-couple lipids to theromstat - MARTINI force-field
On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. m.h.weinga...@uu.nl wrote: Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your system seperately I am simulating a mixed dppc:dppg membrane (see below my parameters). Even these two different lipids-types should be coupled separately? (and how about Na+ (Qd particles) and water - also separately?) I would greatly appreciate any comment on this issue. Thanks a lot Markus my parameter: ; Temperature coupling: tcoupl = berendsen ; Groups to couple separately: tc-grps = DPPC DPPG W NAA Protein Generally in membrane protein simulations different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd) -Anirban -- 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] CHARMM36 and Dispersion correction
Hi ALL, I am simulating a membrane protein immersed in a POPC bilayer using CHARMM36 FF in GROMACS 4.5.5. In NVT and NPT (i.e. in equilibration and production runs) should I use the dispersion correction or not (as suggested in some previous posts)? And if NOT using dispersion correction, then should I use vdwtype as switch? Any suggestion is welcome. Regards, Anirban -- 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] CHARMM36 format POPC
Hi ALL, I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one from Dr. Klauda's site ( http://terpconnect.umd.edu/~jbklauda/research/download.html), but that popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 in place of P, etc.) and hence pdb2gmx throws up error when processed with CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC bilayer available online, or can someone provide, please? Thanks a lot in advance. Regards, Anirban -- 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] CHARMM36 format POPC
Thanks a lot Peter. Will try out with this. -Anirban On Wed, May 2, 2012 at 9:42 PM, Peter C. Lai p...@uab.edu wrote: http://uab.hyperfine.info/~pcl/files/popc36/ These were generated for the following work: (please reference): Lai, P.C. and Crasto, C.J. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations Front. Gene. Volume 3 Year 2012 Number 61 DOI: 10.3389/fgene.2012.00061 On 2012-05-02 05:49:17PM +0530, Anirban Ghosh wrote: Hi ALL, I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one from Dr. Klauda's site ( http://terpconnect.umd.edu/~jbklauda/research/download.html), but that popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 in place of P, etc.) and hence pdb2gmx throws up error when processed with CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC bilayer available online, or can someone provide, please? Thanks a lot in advance. Regards, Anirban -- 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 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] POPC: ff53a6 and CHARMM36 formats
Hi ALL, I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions (N, P, C, O) between this two FFs as a result of which pdb2gmx gives error. Can these atom names (hydrogens can be ignored) of my equilibrated POPC bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in advance. Regards, Anirban -- 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] POPC: ff53a6 and CHARMM36 formats
Thanks Angel and Justin. Will try out the options! Regards, -Anirban On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/1/12 8:05 AM, Ángel Piñeiro wrote: I guess there are better solutions but an alternative is to map your bilayer to MARTINI (http://md.chem.rug.nl/**cgmartini/http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE (http://smmb.usc.es/sugarpie/**sugarpie.phphttp://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom CHARMM36. Even simpler would be to fix the offending atom names and build a suitable .hdb entry (if one does not already exist) and produce the topology with pdb2gmx. I would think it would then be far easier to preserve the original configurations of the lipids, rather than changing the resolution back and forth. -Justin Hope it helps, Ángel. On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote: Hi ALL, I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions (N, P, C, O) between this two FFs as a result of which pdb2gmx gives error. Can these atom names (hydrogens can be ignored) of my equilibrated POPC bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-us...@gromacs.org mailto: gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive athttp://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 togmx-users-request@gromacs.**orgtogmx-users-requ...@gromacs.org mailto: gmx-users-request@**gromacs.org gmx-users-requ...@gromacs.org. Can't post? Readhttp://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 http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding error
On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana paluso...@gmail.comwrote: Respected Sir, While i am running the gromacs software to simulate the protein i am getting the following error. Fatal error: Residue 'GNP' not found in residue topology database http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban Suryanarayna Seera, PhD student. -- 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] Question about starting Gromacs 4.5.4 parallel runs using mpirun
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to start parallel runs without calling mpirun. So on version 4.5.5, I can start a job on eight CPUs using simply the command: mdrun -s topol.tpr -nt 8 However, now I am using a different node on my department's cluster, and this node instead has Gromacs 4.5.4 (compiled without automatic threading). So, I must use mpirun to start parallel runs. I have tried this command: mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with --enable-mpi option? -Anirban where mymachines is an (extensionless) file containing only the text c60 slots=8. (c60 is the name of the node that I am using.) I get this error message: Missing: program name. Program mdrun either does not exist, is not executable, or is an erroneous argument to mpirun. This is strange, because mdrun is, I think, in my path. For example, if I type mdrun -h, I get the manual page for mdrun (version 4.5.4). Then I tried the command which mdrun, and it gave me this output: /usr/local/gromacs/bin/mdrun So, next I tried to call mdrun via mpirun using the specific path for mdrun: mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s topol.tpr This starts running my simulation, but when I look in top, the simulation is only running on a single CPU; there is only one entry for mdrun in top, and it has only %CPU=100 (not eight different entries for mdrun, nor one entry with %CPU=800). Also, the simulation is going at the speed I would expect for running on a single CPU -- it is very slow, so I am convinced that, as top suggests, mdrun is running on only one CPU. Strangely, my colleagues are able to run jobs in parallel using the exact commands that I described above. So apparently something is wrong with my user ID, although there are no error messages (except the error message about Missing: program name that I described). If you have time, do you have any suggestions for other things that I can try? Do you think that something could be wrong with my bashrc file? Thanks for your time! Andrew DeYoung Carnegie Mellon University -- 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] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 1:01 PM, Bala S think_bey...@aol.com wrote: Dear Justin Thanks for the explanation. I am following your tutorial of KALP membrane simulation. I am stuck in between two steps of InflateGRO. After the first step, the tutorial requests to perform EM. Should I be running grompp with new system_inflated.gro file to generate a new .tpr file for EM or should I perform EM with em.tpr which was generated some time back in the tutorial? You should run grompp with the inflated .gro file (system_inflated.gro) since you will be minimizing the inflated .gro file after every compression step to remove bad contacts. The earlier em.tpr was used to remove periodicity of the bilayer only. The latter ran EM but the former shows error 'number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top, 17403) The difference in atom numbers might be because your .top file contains some extra molecules in the [ molecules ] section (may be SOL). Use .top file that contains only protein and lipid molecules. Thanks. Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Regarding errors
On Fri, Apr 27, 2012 at 3:17 PM, seera suryanarayana paluso...@gmail.comwrote: Respected Sir, While i am running gromacs software i am getting the following error.Kindly knowing me how to over come the error. Fatal error: number of coordinates in coordinate file (1cys_ion.gro, 99670) does not match topology (1cys.top, 99680) Your .top file contains 10 extra atoms than you .gro file. Check whether any ion has been mentioned twice by mistake in the .top file. SURYANARAYANA SEERA, PhD student. -- 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] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 3:27 PM, Bala S think_bey...@aol.com wrote: Thank you for that clarification. I found that there were SOL molecules in .top file. I could run the EM now. Coming to the Solvation step, I'm facing a problem. I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat locally. While adding the solvent molecules, what command should I be using? I am using the usual command I use for non-membrane simulations, $ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic followed by $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top When you mention -bt cubic, it adds a cubic water box all around your system (if you visualize you will see your entire bilayer immersed in a cubic water box like a normal protein solvation). But that is wrong. You need to add water only on either side of the lipid membrane (that is along the z-axis only). So use the -box option with editconf without using -c and -d. You can have a look at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly mentioned over there how to go about it. calculation goes for long time showing a huge number of SOL molecules. I guess I'm worng somehere. Thanks. Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/27/12 6:40 AM, Bala S wrote: Thanks for the reply. I'm following the tutorial. Please clarify whether you're using Anirban's or mine. Now that two exist, people will have to be a fair bit more specific :) In your system, to solvate it you have the values that was used during the protien insertion into the bilayer. Following it, I have used the following commandfor my system where the protein is very much smaller than the length of the bilayer. $ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650 $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top If you have to manipulate the box of any coordinate file produced by InflateGRO, whatever you're doing is wrong. You should not be solvating anything until the very last step of the procedure, where your bilayer is of correct size and APL. Exactly, solvate at the end of all the compression steps performed by InflateGro (may be 10 or 20 depending on your system) and minimizations (of only protein + lipid) until you have reached the correct area per lipid. And then only solvate. Check for the dimensions in the last line of the FINAL (compressed and minimized) .gro file and then solvate Thanks, Anirban But I could see in the visualizer that SOL molecules were added on top and bottom but only 1/3 of the length of the bilayer. How to add SOL molecules to whole length or how to remove not-solvated part of lipids? This outcome is a consequence of re-adjusting the box size of a system that likely has other dimensions. As far as I can tell, you shouldn't be doing this. -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/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 http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 6:31 PM, Bala S think_bey...@aol.com wrote: Justin, OOPS!! Sorry for that.. Now I could realize it. Following up.. I have done further iterations with inflategro and reached 0.62 nm^2 which similar to what you have explained in the tutorial. Now, I could see the lipid bilayer really shrinked and no SOL molecules are seen in between. Now the issue I would like to have clarification on is that only 163 SOL molecules were added up and down which looks very scarce for the simulation. What is the solution? First visualize and see whether the hydrophilic ends of the lipid bilayer and your protein's part on either side of the bilayer (like a GPCR's intra and extra cellular ends) are well immersed in the water box. If not, you can increase the solvation box along the z-axis by increasing the z value for -box option in editconf (keeping x and y values same). Anirban Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 7:00 PM, Bala S think_bey...@aol.com wrote: Anirban, Thank you. You guys are doing miracles with the biomolecules and solving almost all of my problems. I have followed your suggestion and could see now some more SOL molecules by increasing the z value. But I am seeing a substantial gap between the surface of the lipid bilayer and added SOL molecules in the visualizer. Is it normal or I have to do something about it? I didn't really get your point. From the surface means on either side of the leaflets? Or one thing you can do is to carry out the EM, and equilibration runs (NVT and NPT) (restraining the protein) and see how the waters orient them with respect to the bilayer. Anirban Thanks Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/27/12 10:00 AM, Bala S wrote: Anirban, Exactly.. That's the gap (either side of the leaflets) I was mentioning about. I'll try EM and check itagain. EM won't fill in solvent gaps. If you're using my protocol for increasing the C radius in vdwradii.dat, then a small gap is normal and will close when doing equilibration as the solvent fills in around the lipid headgroups. Yes, as Justin mentioned, the equilibration runs (restraining the protein) will fill those gaps. Anirban -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/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 http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban On Thu, Apr 26, 2012 at 3:08 PM, Albert mailmd2...@gmail.com wrote: it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban On Thu, Apr 26, 2012 at 3:47 PM, Albert mailmd2...@gmail.com wrote: Hello Anirban: thanks for kind comments. How long did you mean fairly long simulation time ? does 1u ns belongs to this range? CHARMM36 ff is available in gromacs website and we can download it and put them into top directory and then it works. It is not need to make any modification by ourselves. best Albert On 04/26/2012 11:53 AM, Anirban Ghosh wrote: Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, On our cluster I usually get around 25-30 ns/day running on 120 cores (system size around 85K atoms) with PME. Regards, Anirban On Thu, Apr 26, 2012 at 5:28 PM, Albert mailmd2...@gmail.com wrote: Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- 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] Re: GPCR MD Tutorial Using GROMACS (URL)
Hello Bala, Yes, exactly as Justin said it represents just a workflow where a GPCR protein (here B2AR) has been taken as an example. I mentioned it as a GPCR tutorial because many often inquire about GPCR MD simulations only in the forum. But it can be adapted for other membrane proteins as well. And secondly again as Justin mentioned, the choice of lipid depends upon the system you wish to replicate. Regards, Anirban On Thu, Apr 26, 2012 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 9:35 AM, Bala S wrote: Dear Anirban, Thanks for the tutorial you have created for the newbies like me to follow. I wonder the tutorial is only for the GPCRs not applicable for other membrane proteins? Tutorials present possible workflows. Anirban's tutorial does not significantly differ from my own (linked from his) which I happen to know has been applied to many different systems. There is nothing GPCR-specific in this new tutorial, just like there is nothing KALP-specific about mine. I also have another question about slecting a lipidbilayer, what is the criteria is selecting it, for instance popc, dopc or dppc? The choice of lipid depends on what you need to model. -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/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 http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Best Force Field for a Membrane Protein
Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- 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] Best Force Field for a Membrane Protein
Hi ALL, Thanks a lot for the replies. By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the ff43a1 with any membrane protein? Thanks, Anirban On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai p...@uab.edu wrote: Define long simulations? CHARMM27/36 in the sub-100ns timescale works for us. The following paper: Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting Novel Binding Modes of Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. PLoS Comput Biol 7, e1001053 (2011) Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system. On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Membrane Proteins pdb2gmx
Hello Justin, In your membrane protein simulation tutorial after making the topology, you have mentioned that Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide. I suppose this is valid only for the proteins (and not membranes) to be processed through pdb2gmx using gromos53a6_lipid force-field, right? And to process a membrane using pdb2gmx we need to change the aminoacids.rtp file with the relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx use the POPC/DPPC/DSPC.itp file? Thanks a lot. Anirban -- 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] Membrane Proteins pdb2gmx
Hello Peter, Thanks a lot for clarifying my doubt! I have got it right now. Thanks, Anirban On Thu, Dec 8, 2011 at 3:34 PM, Peter C. Lai p...@uab.edu wrote: On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote: Hello Justin, In your membrane protein simulation tutorial after making the topology, you have mentioned that Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide. I suppose this is valid only for the proteins (and not membranes) to be processed through pdb2gmx using gromos53a6_lipid force-field, right? And to process a membrane using pdb2gmx we need to change the aminoacids.rtp file with the relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx use the POPC/DPPC/DSPC.itp file? Yes because in that tutorial, you are not adding an rtp with the lipid residue names to generate lipid topologies from scratch. The tutorial uses pregenerated lipid topologies from Tieleman. You are certainly able to add your own rtp files; pdb2gmx searches all validly formatted rtp files in $GMXLIB/forcefield.ff/ for topology information by residue name. For example, when I converted parts of CGenFF to gromacs, I added my own library of residue types for the small molecules I am modeling as its own .rtp file. (Basically what I mean is, there is no need to hack aminoacids.rtp to add new residues, just add your own .rtp file). However you obtain a topology of a moleculetype (either using pdb2gmx or from someone else e.g. Tieleman) with a given forcefield, you do not need to run pdb2gmx again to generate another topology using that forcefield for subsequent tasks. Just include the relevant .itp file in the .top file you specify to grompp. For example, I generated POPC.itp once and have been using the same file for all my simulations involving POPC. Here is an entire membrane protein+lipid+water+ligand .top ready for grompp -p (I use charmm36 with cgenff added - this is analogous to Justin's gromos53a6_lipid modification): #include charmm36cgen.ff/forcefield.itp #include gpcr.itp #include popc.itp #include charmm36cgen.ff/tips3p.itp #include charmm36cgen.ff/ions.itp #include ligand.itp [ system ] ; Name GPCR in POPC with LIGAND [ molecules ] GPCR 1 ; the gpcr.itp file starts with: ; [ moleculetype ] ; ; Namenrexcl ; GPCR 3 POPC 230 SOL 21468 NA 2 LIGAND 1 gpcr.itp, popc.itp, and ligand.itp were all originally generated by me using pdb2gmx on the relevant molecules coordinate files at one point or another. Again, these individual .itp files are reusable for other simulations involving the same molecule types, protonation states, and charmm36cgen.ff. Hope that helps. -- == 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 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] CPHMD in GROMACS4.5
Hi ALL, Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5? Any suggestion is welcome. Thanks, Anirban -- 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] g_rdf query
Hi ALL, I am using in calculating the distribution of a solvent around the COM of a protein chain using g_rdf. When I plot the output file (attached) I get a curve which increases first (from 1 to a value of about 2.5) and then decreases to x-axis values ranging from 1 to 5. If I understand correctly then x-axis values represent the radius of calculation around the protein. right? It says r. Whats its unit? And what does the y-axis values stand for? Can someone please explain me the g_rdf plot attached here. Thanks a lot in advance. Regards, Anirban attachment: try_rdf.jpg-- 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] GridMatMD and CGMD
Hi ALL, I have simulated a CGMD system consisting of multiple copies of a CG protein in a CG lipid bilayer using the MARTINI FF for the CG definitions. Can I use GridMatMD program to calculate the area per lipid and other properties in this CG system? Which parameters do I need to alter in the input file for GridMatMD in order to properly recognize the CG lipids? Thanks a lot in advance. Regards, Anirban -- 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] GridMatMD and CGMD
Hello Justin, Thanks for the reply. Actually I am using the last frame .gro of a 3 micro-second run CGMD simulation as the input for GridMatMD. But in the thickness plot the positions of the protein depicted are not matching with what I am visualizing through VMD. I suppose this is because of some PBC issue. What -pbc options should I use to generate a proper .gro file to be used as input for GridMatMD? Thanks a lot again. Regards, Anirban On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have simulated a CGMD system consisting of multiple copies of a CG protein in a CG lipid bilayer using the MARTINI FF for the CG definitions. Can I use GridMatMD program to calculate the area per lipid and other properties in this CG system? Which parameters do I need to alter in the input file for GridMatMD in order to properly recognize the CG lipids? CG lipids should work like any other - specify their name in the input file, and the atom name that should be used as a reference point. We have never tested GridMAT-MD with a CG membrane, but it should work the same way as an atomistic membrane. Please let me know if you encounter any problems. -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 -- 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 -pbc option of trjconv
Hi ALL, I have a long simulation trajectory of 3 micro-seconds of multiple protein monomers in a lipid bilayer. Which -pbc option should be used with trjconv to process the trajectory before carrying out any analysis? I am using -pbc nojump, is it correct? Or should I use -pbc whole? Thanks a lot in advance. Thanks, Anirban -- 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] g_sas query
Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- 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 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] g_sas query
Hello Tsjerk Mark, Thanks for the reply. Actually more important than the ions is the lipid bilayer of my system. Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to calculate the SASA of my protein, so should I use a group (Protein+Lipid+Ions) as the calculation group and Protein as the output group? Thanks again, Anirban On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/05/2011 4:36 PM, Anirban Ghosh wrote: Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Only you know where your ions are, and whether their contribution to surface area means anything. Make the hybrid groups accordingly. Mark Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- 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 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] g_sas query
Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- 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] trjcat error of different spacing
Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 ps WARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. Thanks, Anirban -- 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] trjcat error of different spacing
Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 psWARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -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 -- 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] trjcat error of different spacing
Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Thanks, Anirban On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? I don't know yet. A few more questions: 1. What version of Gromacs are you using? 2. How many total trajectories are you concatenating? You said there was a problem from 10 - 300 ns, but I don't see any times shown here below 2957280. The real problem could be early on in the trajectory. -Justin Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 - frame 10 time 300.000 ps - frame 99980 time 2999400.000 psWARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. What does gmxcheck tell you about each of the individual trajectories (prior to running trjcat)? -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 -- gmx-users mailing listgmx-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 -- 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
[gmx-users] CG to FG transformation error
Hi, I have successfully converted my CG (only) protein model to FG model using g_fg2cg command of the gromacs_reverse package. But now when I try to compile my .mdp file for SA run, grompp is throwing some warnings: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# WARNING 1 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_force' in parameter file WARNING 2 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_a' in parameter file WARNING 3 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... processing topology... - My system contains only multiple copies of a protein. How to solve this issue? Any suggestion is welcome. Thanks, -Anirban -- 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] Error: No such moleculetype Protein
Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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] Error: No such moleculetype Protein
Hi Tsjerk, Thanks for the reply. Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using: g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro So do I need to supply any other parameter to this command or how to mention this refering of 'Protein' group here. Thanks, Anirban On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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 -- 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 -- 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] Error: No such moleculetype Protein
Hi, I have worked around the problem. I was not including a .itp file. But now I am getting Segmentation Fault: Excluding 1 bonded neighbours for DSPC 104 Excluding 1 bonded neighbours for W 1397 Excluding 1 bonded neighbours for NA+ 0 Excluding 1 bonded neighbours for CL- 4 Number of fg atoms 410288 Number of cg atoms 57296 Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms. Reading frame 0 time0.000 1297343010 Segmentation fault Why is this happening? Thanks, Anirban On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi Tsjerk, Thanks for the reply. Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using: g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro So do I need to supply any other parameter to this command or how to mention this refering of 'Protein' group here. Thanks, Anirban On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- 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 -- 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 -- 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] DSPC all atom .itp file
Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- 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] CG to FG transformation error
Hi, I am trying to convert a coarse grained protein to a full atom model after CGMD. I am using the modified gromacs_reverse code available from MARTINI site. I am using the following command: g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro But in the output full.gro all the atoms are having coordinate values as 0.00. My pro_cg.top file looks like: #define _FF_GROMOS96 #define _FF_GROMOS42A2 ;#define _FF_GROMACS ;#define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.125 0.5 #include ffG43a2nb.itp #include ffG43a2bon.itp Is this correct? where I am going wrong? I think the problem is with pro_cg.top file only. Any suggestion is welcome. Thanks, -Anirban -- 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] DSPC all atom .itp file
Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- 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] g_lie query
Thanks a lot Justin for the reply. So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? And why am I getting only a single value of DGbind for all the frames captured in the .edr file? Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values. I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run. -Justin Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- 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 listgmx-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/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/mailing_lists/users.php -- 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 -- 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] g_lie query
Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something? Thanks a lot again. Anirban On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? Again I would ask you to not rely entirely upon my advice for this. I have only examined the LIE method sparingly. My best answer is, probably, but do read the literature on the method to be sure. And why am I getting only a single value of DGbind for all the frames captured in the .edr file? The lie.xvg file contains the LIE values as a function of time. What's printed to the screen is the average value and standard deviation. -Justin Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values. I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run. -Justin Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- 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 -- gmx-users mailing listgmx-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 Please search the archive at http://www.gromacs.org/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 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/mailing_lists/users.php -- 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 listgmx-users@gromacs.org
Re: [gmx-users] g_lie query
Thanks a lot Justin !!! --Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something? If the interactions of your ligand and its receptor are stable, then there may be no change in the energetics. I don't know anything about your system, so I can't say anything beyond that. -Justin Thanks a lot again. Anirban On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? Again I would ask you to not rely entirely upon my advice for this. I have only examined the LIE method sparingly. My best answer is, probably, but do read the literature on the method to be sure. And why am I getting only a single value of DGbind for all the frames captured in the .edr file? The lie.xvg file contains the LIE values as a function of time. What's printed to the screen is the average value and standard deviation. -Justin Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values. I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run. -Justin Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- 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 http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] g_lie query
Thanks a lot Justin for the reply !!! While calculating the Elj and Eqq values should we consider the short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in the .edr file? And for Coulomb also? Which one should we consider? Thanks again. Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something? If the interactions of your ligand and its receptor are stable, then there may be no change in the energetics. I don't know anything about your system, so I can't say anything beyond that. -Justin Thanks a lot again. Anirban On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? Again I would ask you to not rely entirely upon my advice for this. I have only examined the LIE method sparingly. My best answer is, probably, but do read the literature on the method to be sure. And why am I getting only a single value of DGbind for all the frames captured in the .edr file? The lie.xvg file contains the LIE values as a function of time. What's printed to the screen is the average value and standard deviation. -Justin Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values. I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run. -Justin Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
Re: [gmx-users] g_lie query
Thanks Justin. Yes I did use PME during the simulations. But still when I process the .edr file with g_energy, it gives both the options...LJ-1-4 and LJ(SR). So if I am not wrong, I should be using the LJ(SR) value as the Elj in the LIE calculation. Right? Thanks again. Anirban On Tue, Dec 28, 2010 at 11:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply !!! While calculating the Elj and Eqq values should we consider the short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in 1-4 interactions are intramolecular, thus should not be relevant to the LIE calculation. the .edr file? And for Coulomb also? Which one should we consider? Did you use PME? If so, you can't break down the Coulombic terms entirely. -Justin Thanks again. Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something? If the interactions of your ligand and its receptor are stable, then there may be no change in the energetics. I don't know anything about your system, so I can't say anything beyond that. -Justin Thanks a lot again. Anirban On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? Again I would ask you to not rely entirely upon my advice for this. I have only examined the LIE method sparingly. My best answer is, probably, but do read the literature on the method to be sure. And why am I getting only a single value of DGbind for all the frames captured in the .edr file? The lie.xvg file contains the LIE values as a function of time. What's printed to the screen is the average value and standard deviation. -Justin Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values. I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run. -Justin Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu
[gmx-users] Energy due to Hydrogen bonds
Hi ALL, Is there any means to calculate the total energy arising due to the breaking and formation for hydrogen bonds only in GROMACS? Does the .edr file contains this information? If yes then how to parse it? I don't think the .log file records this value. Any suggestion is welcome. Thanks, Anirban -- 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] g_lie query
Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Go to the literature and understand what information is needed for such a simulation, and then look into the list archives and you'll find dozens of threads about using g_lie. -Justin Regards, Anirban -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] Which .tpr file to use for g_rms?
Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- 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 -- 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] Which .tpr file to use for g_rms?
Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Thanks again. Anirban On 12/4/10, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- 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 listgmx-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 -- 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 -- 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] Which .tpr file to use for g_rms?
Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump So which .tpr file should I use? Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Since you're not using the coordinates in the .tpr file to extract the last frame and map its coordinates onto the .tpr's atom names, it can't matter what they are. Mark Thanks again. Anirban On 12/4/10, Justin A. Lemkuljalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 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 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 -- 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 -- 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
[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero
Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] Free Energy Calculation: dVpot/dlambda is always zero
Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] Free Energy Calculation: dVpot/dlambda is always zero
Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltypecouple-lambda0couple-intramolThanks a lot again. Regards, Anirban On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. You haven't indicated your Gromacs version, but assuming you're using something in the 4.x series, you're not specifying the necessary parameters to do any sort of transformation, particularly couple_lambda0 and couple_lambda1. If left at their default values (vdw-q), nothing gets decoupled. -Justin Regards, Anirban -- 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 -- 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] WHAM
Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format? Any suggestion in this regard is welcome. Regards, Anirban -- 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] WHAM
Hi Justin, Thanks a lot for the reply. Yes I have had a look at section 4.4.2. But section 5.3 tells that this WHAM can be used with the REMD data set as well. So my question is that how to present this REMD data of multiple trajectories as input to WHAM? Do I need to work around with the WHAM code or there is some other way? Any suggestion is welcome. Thanks again. Regards, Anirban On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format? Any suggestion in this regard is welcome. I would suggest you consult the documentation for the program (i.e. the Grossfield WHAM manual, section 4.2.2). I don't know how you intend to pass your data to a program that is designed for umbrella sampling, but I suppose that's your task. -Justin Regards, Anirban -- 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 -- 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] Bioinformatics Symposium at C-DAC, Pune
The Bioinformatics Group at C-DAC, Pune is going to organize a Symposium on Accelerating Biology from December 14-16 2010 at VITS, Pune. You can register for the same at: http://pune.cdac.in/html/events/bioinfo/accelerating_biology/index.aspx Regards, -- Anirban Ghosh C-DAC, Pune, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih.LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total EnergyTemperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Regards, Anirban attachment: sim.jpeg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Thanks a lot XAvier for clarifying my doubt. You mean to say -rdd option with mdrun, right? And why does this curvature of the membrane occurs? Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole x.peri...@rug.nl wrote: Although a bit worrying the curvature of your bilayer is not responsible for the error message you are seeing. to solve the problem you have to increase to use the -rrd option (see manual for explanation). Typicaly a value of 1.4 to 1.6 should be fine. On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote: Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih.LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total EnergyTemperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Regards, Anirban sim.jpeg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Centre of mass removal in CGMD
Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the centre of mass removal component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Centre of mass removal in CGMD
Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole x.peri...@rug.nl wrote: On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the centre of mass removal component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - This is the way to go :)) Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Removing water from a trajectory
Hi ALL, I have a system consisting of protein+lipid+ligand+water which has been simulated for 10 ns. Now I want to make a compressed trajectory from the original one by keeping only the protein and the ligand. I am trying to do so by using trjconv with an index file. But every time trjconv is showing the default options and I am not able to select the protein and the ligand simultaneously to generate the output. How can I do this? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Helix Tilt Calculation
Thanks XAvier and George for the reply. Yes the N and C terminus are on the opposite sides of the bilayer. So I can take the values of the even TMs as (180 - respective value), correct? Regards, Anirban On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili gek2...@med.cornell.eduwrote: Hi, Your 150 degree angle is in reality 30 degrees (180-30). This is a matter of defining the vector representing your helix vs. the direction of the z axis. If your vector points in the opposite direction of the z axis, then your angle will be between 90 and 180 degrees. George Anirban Ghosh wrote: Hi ALL, I am using g_angle to calculate the tilt of individual helix in a rhodopsin GPCR with respect to z axis. In the index file I am defining the top and bottom of each helix with first 4 and last 4 residues of that helix respectively. Strangely, I am getting the tilt angle of the odd helices like TM1, 3 and 5 in the range of 30 degrees, but the even helices TM2, 4 and 6 are giving value in the range of 150 degrees. But visual inspection of the simulation does not show such huge deviation. Why is it giving so? Am I doing anything wrong here? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA gek2...@med.cornell.edu Phone: 1-212-746-6539 Fax: 1-212-746-6226 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Helix Tilt Calculation
Thanks a lot XAvier! On Sat, Jun 5, 2010 at 2:10 PM, XAvier Periole x.peri...@rug.nl wrote: Yes, or inverse your sections from the index! On Jun 5, 2010, at 10:10 AM, Anirban Ghosh wrote: Thanks XAvier and George for the reply. Yes the N and C terminus are on the opposite sides of the bilayer. So I can take the values of the even TMs as (180 - respective value), correct? Regards, Anirban On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili gek2...@med.cornell.edu wrote: Hi, Your 150 degree angle is in reality 30 degrees (180-30). This is a matter of defining the vector representing your helix vs. the direction of the z axis. If your vector points in the opposite direction of the z axis, then your angle will be between 90 and 180 degrees. George Anirban Ghosh wrote: Hi ALL, I am using g_angle to calculate the tilt of individual helix in a rhodopsin GPCR with respect to z axis. In the index file I am defining the top and bottom of each helix with first 4 and last 4 residues of that helix respectively. Strangely, I am getting the tilt angle of the odd helices like TM1, 3 and 5 in the range of 30 degrees, but the even helices TM2, 4 and 6 are giving value in the range of 150 degrees. But visual inspection of the simulation does not show such huge deviation. Why is it giving so? Am I doing anything wrong here? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA gek2...@med.cornell.edu Phone: 1-212-746-6539 Fax: 1-212-746-6226 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Helix Tilt Calculation
Hi ALL, I am using g_angle to calculate the tilt of individual helix in a rhodopsin GPCR with respect to z axis. In the index file I am defining the top and bottom of each helix with first 4 and last 4 residues of that helix respectively. Strangely, I am getting the tilt angle of the odd helices like TM1, 3 and 5 in the range of 30 degrees, but the even helices TM2, 4 and 6 are giving value in the range of 150 degrees. But visual inspection of the simulation does not show such huge deviation. Why is it giving so? Am I doing anything wrong here? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_helixorient issue
Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0. --- # # g_helixorient is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Cumulative local helix tilt @xaxis label Time(ps) @yaxis label Tilt (degrees) @TYPE xy 2 03.595408201224.23953723907 5.74576044083 5.64022207262.993204355243.96751046181 6.915472984316.317507743845.708302021031.80687570572 7.904520511635.554297924044.3107757568413.4955091476 10.86933803566.696783542631.318642735488.81209087372 15.092011451716.443498611513.575768470812.6605091095 9.89414119725.959523200992.222523212434.23878717422 11.912554740915.239257812510.13733291632.50473761559 2.987089633940 4 0 0.1932501047851.85375285149 4.660104274755.734657764433.596650362013.71966171265 5.862170696265.205702304844.286367416385.67181348801 11.8561506271 10.8149480825.253306865693.01665711403 3.188149690636.1265802383410.878685951213.1984567642 15.8662624359 17.9544162759.977549552923.82837629318 7.255657672884.875072002413.158228397375.81644439697 6.565203189857.591495513925.399117946622.35803961754 4.941868305210 6.0047684 02.78084087372 2.5538725853 3.536648511898.4336194992114.915288925213.8589410782 6.6992340087911.7872600555 17.235452652 10.804684639 12.89069366468.979190826425.7719144821210.7680120468 9.713017463688.8874626159711.251163482710.2795152664 8.691395759587.554894447333.242376565931.74266982079 2.973826408394.069952487953.690156698232.21045541763 2.921667337424.463324546814.281089782713.39760541916 4.103402614590 8 0 5.4110045433 5.6742272377 8.93139266968 11.787487038.761271476755.92636489868 2.527382135396.2623438835110.01829242712.88692927361 8.243747711184.966527462018.7450408935517.1016178131 14.6491327286 8.43484878549.4807758331311.1341199875 11.373338699314.302871704112.88017845157.42469358444 3.84174942974.058297157291.937186241152.07590007782 6.721652030949.818412780769.60572147369 6.2793135643 4.37946939468 --- How to visualize this file properly? Why is the .xvg file written in this manner? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_helixorient issue
Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0. --- # # g_helixorient is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Cumulative local helix tilt @xaxis label Time(ps) @yaxis label Tilt (degrees) @TYPE xy 2 03.595408201224.23953723907 5.74576044083 5.64022207262.993204355243.96751046181 6.915472984316.317507743845.708302021031.80687570572 7.904520511635.554297924044.3107757568413.4955091476 10.86933803566.696783542631.318642735488.81209087372 15.092011451716.443498611513.575768470812.6605091095 9.89414119725.959523200992.222523212434.23878717422 11.912554740915.239257812510.13733291632.50473761559 2.987089633940 4 0 0.1932501047851.85375285149 4.660104274755.734657764433.596650362013.71966171265 5.862170696265.205702304844.286367416385.67181348801 11.8561506271 10.8149480825.253306865693.01665711403 3.188149690636.1265802383410.878685951213.1984567642 15.8662624359 17.9544162759.977549552923.82837629318 7.255657672884.875072002413.158228397375.81644439697 6.565203189857.591495513925.399117946622.35803961754 4.941868305210 6.0047684 02.78084087372 2.5538725853 3.536648511898.4336194992114.915288925213.8589410782 6.6992340087911.7872600555 17.235452652 10.804684639 12.89069366468.979190826425.7719144821210.7680120468 9.713017463688.8874626159711.251163482710.2795152664 8.691395759587.554894447333.242376565931.74266982079 2.973826408394.069952487953.690156698232.21045541763 2.921667337424.463324546814.281089782713.39760541916 4.103402614590 8 0 5.4110045433 5.6742272377 8.93139266968 11.787487038.761271476755.92636489868 2.527382135396.2623438835110.01829242712.88692927361 8.243747711184.966527462018.7450408935517.1016178131 14.6491327286 8.43484878549.4807758331311.1341199875 11.373338699314.302871704112.88017845157.42469358444 3.84174942974.058297157291.937186241152.07590007782 6.721652030949.818412780769.60572147369 6.2793135643 4.37946939468 --- How to visualize this file properly? Why is the .xvg file written in this manner? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_helixorient issue
Hi ALL, I am trying to find out the tilt of a helix during a simulation. I am using g_helixorient with the -otilt option. However I am getting the following output, which when plotted using xmgrace, gives a straight along y=0. --- # # g_helixorient is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Cumulative local helix tilt @xaxis label Time(ps) @yaxis label Tilt (degrees) @TYPE xy 2 03.595408201224.23953723907 5.74576044083 5.64022207262.993204355243.96751046181 6.915472984316.317507743845.708302021031.80687570572 7.904520511635.554297924044.3107757568413.4955091476 10.86933803566.696783542631.318642735488.81209087372 15.092011451716.443498611513.575768470812.6605091095 9.89414119725.959523200992.222523212434.23878717422 11.912554740915.239257812510.13733291632.50473761559 2.987089633940 4 0 0.1932501047851.85375285149 4.660104274755.734657764433.596650362013.71966171265 5.862170696265.205702304844.286367416385.67181348801 11.8561506271 10.8149480825.253306865693.01665711403 3.188149690636.1265802383410.878685951213.1984567642 15.8662624359 17.9544162759.977549552923.82837629318 7.255657672884.875072002413.158228397375.81644439697 6.565203189857.591495513925.399117946622.35803961754 4.941868305210 6.0047684 02.78084087372 2.5538725853 3.536648511898.4336194992114.915288925213.8589410782 6.6992340087911.7872600555 17.235452652 10.804684639 12.89069366468.979190826425.7719144821210.7680120468 9.713017463688.8874626159711.251163482710.2795152664 8.691395759587.554894447333.242376565931.74266982079 2.973826408394.069952487953.690156698232.21045541763 2.921667337424.463324546814.281089782713.39760541916 4.103402614590 8 0 5.4110045433 5.6742272377 8.93139266968 11.787487038.761271476755.92636489868 2.527382135396.2623438835110.01829242712.88692927361 8.243747711184.966527462018.7450408935517.1016178131 14.6491327286 8.43484878549.4807758331311.1341199875 11.373338699314.302871704112.88017845157.42469358444 3.84174942974.058297157291.937186241152.07590007782 6.721652030949.818412780769.60572147369 6.2793135643 4.37946939468 --- How to visualize this file properly? Why is the .xvg file written in this manner? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_bundle issue
Hi ALL, I tried to calculate the helix tilt of a single helix (TM5) among 7 helices using g_bundle. In the index file I defined the two groups (top bottom) as the C-alpha of the first 5 and last 5 residues of TM5 respectively. But in the bun_tilt.xvg file I am getting the values as: --- # This file was created Thu May 20 15:29:50 2010 # by the following command: # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1 # # g_bundle is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Axis tilts @xaxis label Time (ps) @yaxis label (degrees) @TYPE xy 0 0 2 0.0197823 4 0 6 0.0197823 8 0 10 0 12 0.0197823 14 0 16 0.0197823 18 0 20 0.0279765 22 0 24 0 26 0.0197823 28 0 30 0 32 0 34 0 36 0 38 0.0197823 And when plotted it gives a blank plot. Why it is coming like this? Am I doing anything wrong? Any suggestion is welcome. The contents of the index file is: [ top ] 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Selecting groups for analysis in batch submission
Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Selecting groups for analysis in batch submission
Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selecting groups for analysis in batch submission
Thanks a lot Justin. On Tue, May 18, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Regards, Anirban -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PCA component
Hi ALL, I am trying to do a PCA for my simulation. I generated a covarience matrix using g_covar and now I want to visualize the motion only along first principal component. So with g_anaeig I gave the option -first 1 -last 1. But it gave the error as: Fatal error: You have selected less than 3 eigenvectors Cant I generate the projections and filtered trajectories along only one PC? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PCA component
Hi ALL, I am trying to do a PCA for my simulation. I generated a covarience matrix using g_covar and now I want to visualize the motion only along first principal component. So with g_anaeig I gave the option -first 1 -last 1. But it gave the error as: Fatal error: You have selected less than 3 eigenvectors Cant I generate the projections and filtered trajectories along only one PC? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hydrogen Bond Residence Time
Hi ALL, How can I obtain the residence time of each hydrogen bond during a simulation? I think the -hbn and -hbm options of g_hbond has to be used, but how? Is there any script to extract that data? And what is the difference between the residence time and the life time of a hydrogen bond? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hydrogen Bond Residence Time
Hi ALL, How can I obtain the residence time of each hydrogen bond during a simulation? I think the -hbn and -hbm options of g_hbond has to be used, but how? Is there any script to extract that data? And what is the difference between the residence time and the life time of a hydrogen bond? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Remove water from trajectory
Hi ALL, I just want to convert my trajectory (.trr) to a compressed .xtc format after removing water from it. trjconv has to be used for this. I just want to know should I use an index file to exclude the water from the trajectory or is there any other option to be given with trjconv to write out a trajectory without water? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Freezing a portion of a protein during simulation
Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp
Re: [gmx-users] Simulation of ONLY Lipid Bilayer
On Thu, Apr 29, 2010 at 3:29 PM, Saumya samvygu...@gmail.com wrote: Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I need to use strong position restraints (because that is for protein and I am just using the lipid bilayer)? You want to scale the lipid positions to what? InflateGro is used to pack the lipid molecules around a protein, but you want to simulate only lipids, so no point in using it. If you want to simulate a lipid bilayer, you can continue with one taken from Tieleman's site (but with what objective?). After the script is run, When I try doing the energy minimization, it shows unequal number of atoms in .gro and topology file. (the GRO Input has only lipid molecules where as topology files takes into account both SOL and lipid molecules). How to remove this error? InflateGro always removes all water (SOL) molecules. So you need to resolvate the bilayer and update your .top file accordingly. Go through the manual once. I am unable to find any tutorial that could guide through the steps and the parameters to be set while doing the simulation of only bilayers. Please suggest some tutorial. Kindly guide through the steps. Regards, Saumya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Freezing a portion of a protein during simulation
Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp
[gmx-users] Freezing a portion of a protein during simulation
Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Regards, Anirban On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance. If your protein is still moving, then you aren't correctly applying your position restraints. Without seeing your topology and .mdp file, there's no way to know what you're doing wrong. You can also use the freezegrps option in the .mdp file, but then you also have to make sure you're using the appropriate energygrp_excl, etc. It is generally much easier to apply position restraints. -Justin Regards, Anirban -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Freezing a portion of a protein during simulation
Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp file
[gmx-users] Normal Mode Analysis
Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using nm as the integrator? For how long should I run this MD with nm integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Normal Mode Analysis
Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using nm as the integrator? For how long should I run this MD with nm integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Freezing a portion of a protein during simulation
Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Regards, Anirban On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance. If your protein is still moving, then you aren't correctly applying your position restraints. Without seeing your topology and .mdp file, there's no way to know what you're doing wrong. You can also use the freezegrps option in the .mdp file, but then you also have to make sure you're using the appropriate energygrp_excl, etc. It is generally much easier to apply position restraints. -Justin Regards, Anirban -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Freezing a portion of a protein during simulation
Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hydrogens missing during parameterization
Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogens missing during parameterization
Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welcome. Thanks a lot for the prompt reply. Regards, Anirban On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole x.peri...@rug.nl wrote: You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http
