[gmx-users] mismatch between energies of sequential minimization runs
Hi, I am running 2 sequential minimizations with the same mdp file. As expected the second minimization stops in step zero and the resulting structures of the 2 minimization runs are identical (RMSD=0.0). But, the energies of the last step of the first minimization (step 14) and the zero step of the second minimization are not identical (see below). What could be the reason for this mismatch? Thanks, Efrat First minimization: Step Time Lambda 14 14.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. Improper Dih. LJ-14 1.95260e+011.32951e+021.29144e+023.99233e-014.69282e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Pressure (bar) -3.24612e+03 -3.33371e+014.24793e+031.29742e+030.0e+00 Second minimization: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. Improper Dih. LJ-14 2.24603e+011.31903e+021.29221e+023.98797e-014.61009e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Pressure (bar) -3.24585e+03 -3.32600e+014.24778e+031.29876e+030.0e+00 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: simulation of a metal binding sites
Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
On Wed, Feb 16, 2011 at 2:44 PM, Gerrit Groenhof ggro...@gwdg.de wrote: What is your path to the gaussian executable? GAUSS_EXE=/software/g03gromacs/g03 GAUSS_DIR=/software/g03gromacs/g03 In this directories are all gaussian l*.exe files. DEVEL_DIR=/software/g03gromacs/g03/modlinks Txema Gerrit On 16 Feb 2011, at 14:39, Txema Mercero wrote: I get the same error which I attach this time: - Back Off! I just backed up md.log to ./#md.log.8# Reading file topol.tpr, VERSION 4.5.3 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 24 QMlevel: RHF/6-31G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 /software/g03Gromacs/g03gaussian initialised... Back Off! I just backed up traj.trr to ./#traj.trr.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 *** glibc detected *** /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun: malloc(): memory corruption: 0x077711b0 *** === Backtrace: = /lib64/libc.so.6[0x3ddcc724ac] /lib64/libc.so.6(__libc_calloc+0xc0)[0x3ddcc73ce0] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6(save_calloc+0x32)[0x2b0e5ba08462] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(call_gaussian+0x81)[0x2b0e5b38cfd1] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(call_QMroutine+0x25)[0x2b0e5b384265] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(calculate_QMMM+0x665)[0x2b0e5b383bb5] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_force_lowlevel+0xd9)[0x2b0e5b2fcbd9] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_force+0xdaf)[0x2b0e5b35ae6f] /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_steep+0x7d6)[0x2b0e5b314a26] /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun[0x4149ba] /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun[0x41dc03] /lib64/libc.so.6(__libc_start_main+0xf4)[0x3ddcc1d974] /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun(do_nm+0x4f1)[0x407069] === Memory map: 0040-0046d000 r-xp 00:18 20054244 /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun 0066d000-00672000 rw-p 0006d000 00:18 20054244 /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun 00672000-00673000 rw-p 00672000 00:00 0 0770a000-077b6000 rw-p 0770a000 00:00 0 [heap] 3ddc80-3ddc81c000 r-xp 08:02 5751044 /lib64/ld-2.5.so 3ddca1b000-3ddca1c000 r--p 0001b000 08:02 5751044 /lib64/ld-2.5.so 3ddca1c000-3ddca1d000 rw-p 0001c000 08:02 5751044 /lib64/ld-2.5.so 3ddcc0-3ddcd4c000 r-xp 08:02 5750905 /lib64/libc-2.5.so 3ddcd4c000-3ddcf4c000 ---p 0014c000 08:02 5750905 /lib64/libc-2.5.so 3ddcf4c000-3ddcf5 r--p 0014c000 08:02 5750905 /lib64/libc-2.5.so 3ddcf5-3ddcf51000 rw-p 0015 08:02 5750905 /lib64/libc-2.5.so 3ddcf51000-3ddcf56000 rw-p 3ddcf51000 00:00 0 3ddd00-3ddd082000 r-xp 08:02 5750931 /lib64/libm-2.5.so 3ddd082000-3ddd281000 ---p 00082000 08:02 5750931 /lib64/libm-2.5.so 3ddd281000-3ddd282000 r--p 00081000 08:02 5750931 /lib64/libm-2.5.so 3ddd282000-3ddd283000 rw-p 00082000 08:02 5750931 /lib64/libm-2.5.so 3ddd40-3ddd402000 r-xp 08:02 5750939 /lib64/libdl-2.5.so 3ddd402000-3ddd602000 ---p 2000 08:02 5750939 /lib64/libdl-2.5.so 3ddd602000-3ddd603000 r--p 2000 08:02 5750939 /lib64/libdl-2.5.so 3ddd603000-3ddd604000 rw-p 3000 08:02 5750939 /lib64/libdl-2.5.so 3ddd80-3ddd816000 r-xp 08:02 5751046 /lib64/libpthread-2.5.so 3ddd816000-3ddda15000 ---p 00016000 08:02 5751046 /lib64/libpthread-2.5.so 3ddda15000-3ddda16000 r--p 00015000 08:02 5751046 /lib64/libpthread-2.5.so 3ddda16000-3ddda17000 rw-p 00016000 08:02 5751046 /lib64/libpthread-2.5.so 3ddda17000-3ddda1b000 rw-p 3ddda17000 00:00 0 3dddc0-3dddc14000 r-xp 08:02 10306767 /usr/lib64/libz.so.1.2.3 3dddc14000-3ddde13000 ---p 00014000 08:02 10306767 /usr/lib64/libz.so.1.2.3 3ddde13000-3ddde14000 rw-p 00013000 08:02 10306767 /usr/lib64/libz.so.1.2.3 3ddfc0-3ddfc15000 r-xp 08:02 5751016 /lib64/libnsl-2.5.so 3ddfc15000-3ddfe14000 ---p 00015000 08:02 5751016 /lib64/libnsl-2.5.so 3ddfe14000-3ddfe15000 r--p 00014000 08:02 5751016 /lib64/libnsl-2.5.so 3ddfe15000-3ddfe16000 rw-p 00015000 08:02 5751016 /lib64/libnsl-2.5.so 3ddfe16000-3ddfe18000 rw-p 3ddfe16000 00:00 0 3de440-3de4533000 r-xp 08:02 10310609 /usr/lib64/libxml2.so.2.6.26 3de4533000-3de4733000 ---p 00133000 08:02 10310609 /usr/lib64/libxml2.so.2.6.26 3de4733000-3de473c000 rw-p 00133000 08:02 10310609 /usr/lib64/libxml2.so.2.6.26 3de473c000-3de473d000 rw-p 3de473c000 00:00 0 3dea20-3dea20d000 r-xp 08:02 5751072
[gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)
2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- 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] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)
Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhof ggro...@gwdg.de wrote: 2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists topol.tpr.gz Description: GNU Zip compressed data -- 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] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)
Hi, With gmx 5.5.3 your input works here. Still it crashes in g09, but that is because you have a multiplicity of 1 with 181 electrons. QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 24 QMlevel: RHF/6-31G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 /home/ggroenh/g09/gaussian initialised... Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps= 1000 Calling '/home/ggroenh/g09//g09 input.com input.log' --- Program mdrun, VERSION 4.5.3 Source code file: qm_gaussian.c, line: 913 Fatal error: Call to '/home/ggroenh/g09//g09 input.com input.log' failed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I Used To Care, But Things Have Changed (Bob Dylan) On 02/17/2011 10:39 AM, Txema Mercero wrote: Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhofggro...@gwdg.de wrote: 2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- 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] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)
Thanks Gerrit, Do you have any guess whether the problem could in in gromacs or Gaussian compilation? In the lines you sent me in your execution I see Calling '/home/ggroenh/g09//g09 input.com input.log But I do not see something like this in our exectution. By the way are there somewhere instruction for g09? Or I can just apply the changes mentioned in http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf ? Thanks for your help. On Thu, Feb 17, 2011 at 10:52 AM, Gerrit Groenhof ggro...@gwdg.de wrote: Hi, With gmx 5.5.3 your input works here. Still it crashes in g09, but that is because you have a multiplicity of 1 with 181 electrons. QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 24 QMlevel: RHF/6-31G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 /home/ggroenh/g09/gaussian initialised... Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 Calling '/home/ggroenh/g09//g09 input.com input.log' --- Program mdrun, VERSION 4.5.3 Source code file: qm_gaussian.c, line: 913 Fatal error: Call to '/home/ggroenh/g09//g09 input.com input.log' failed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I Used To Care, But Things Have Changed (Bob Dylan) On 02/17/2011 10:39 AM, Txema Mercero wrote: Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhofggro...@gwdg.de wrote: 2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Protein-membrane system
Jianguo Li wrote: Hi, 3000 water molecule per lipids per second corresponds to 0.000384 water molecules transferred across the membrane per nano second (assume the system contains 128 lipids). It seems water translocation should not be observed in a simulation of 10 ns, but I am not sure. And I only find one reference paper(Biophysical Journal, Volume 96, 2009, pg4493–4501) about the water translocation across the membrane, in which a asymmetric membrane is used. I also have similar observations for my protein-membrane system. I observed 10~15 times water translocation arosss the membrane during 100 ns simulation when my protein adsorbed on the membrane. I am wondering these water translocation is normal in all-atom simulations or they are due to the protein-induced membrane deformation? Sounds like a job for a proper control. If you see the same translocation in a pure bilayer under the same conditions, then it's not likely to be related to the presence of your protein, but rather an intrinsic feature of the model membrane. -Justin Any comment is highly appreciated, thank you! best regards, Jianguo *From:* Itamar Kass itamar.k...@monash.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 17 February 2011 07:20:19 *Subject:* Re: [gmx-users] Protein-membrane system Dear Aldo, It is totally OK to see water molecules within the bilayer, both in simulations and real life. If I am not totally wrong, 3000 water molecule per lipids per second are being transferred across the bilayer without any protein involvement. If your system is stable, the lipids density profile seems OK as well as its the thickness, you are fine. Cheers, Itamar. On 17/02/11 5:48 AM, Justin A. Lemkul wrote: Aldo Segura wrote: Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such behavior? Membrane protein systems take a long time (tens of ns or maybe more) to equilibrate, so some water may drift in and out during the initial few ns as voids in the lipids open and close. Nothing to worry about, unless for some reason they persist out past the expected equilibration time. -Justin Best regards, *//* */== = Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx mailto:asegu...@ipn.mx mailto:asegu...@ipn.mx mailto:asegu...@ipn.mx; aldoseg...@gmail.com mailto:aldoseg...@gmail.com mailto:aldoseg...@gmail.com mailto:aldoseg...@gmail.com == ===/* -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu mailto:itamar.k...@monash.edu -- 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
Re: [gmx-users] initial structures for md simulations
packmol and hyperchem can do it for u. On Wed, Feb 16, 2011 at 4:57 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/02/2011 11:24 PM, oguz gurbulak wrote: *Dear All*, I want to generate some initial crystalline structures of my target molecules for md simulations. *Are there any free softwares* to do this? Some sources for obtaining initial coordinates can be found here http://www.gromacs.org/Documentation/File_Formats/Coordinate_File. I doubt there is going to be software to generate crystalline structures (whatever you mean by that). You could get a structure and replicate it with (e.g. genconf). And are there any complete sources that give the theoretical structures of organic molecules ( like hydrocarbons ) determined by the experiments and give the x-ray, neutron scattering, NMR, IR or Raman results of organic molecules apart from the articles ? Could you please share your thoughts about this issue ? Theoretical structures you compute according to some model. Experimental data tends to live in original literature and lots of specialist databases. Which do you actually want? Google is your friend either way. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 blank dgdl
Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md with mdp : pbc = xyz energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 50 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.1 rcoulomb= 1.1 ;1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no *** Thank you in advance. Moeed -- 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 blank dgdl
Moeed wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md with mdp : pbc = xyz energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 50 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME By not setting a proper coulombtype, grompp defaults to cutoff, which is a very inaccurate method. vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.1 rcoulomb= 1.1 ;1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no You didn't set couple-moltype so mdrun doesn't know which molecule to decouple. -Justin *** Thank you in advance. Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] free energy blank dgdl
hi It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction. dawei On Thu, Feb 17, 2011 at 8:26 AM, Moeed lecie...@googlemail.com wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr output.grompp_em mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v output.mdrun_em MD grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n PE-HEX.ndx output.grompp_md mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x md-l0.xtc -dgdl md-l0.dgdl -v output.mdrun_md with mdp : pbc = xyz energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 50 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.1 rcoulomb= 1.1 ;1.0 rvdw= 1.0 ;Temperature coupling Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ;0.1 ref_t = 400 ;300 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs ; Free energy control stuff free_energy = yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no *** Thank you in advance. Moeed -- 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] mismatch between energies of sequential minimization runs
On 17/02/2011 6:47 PM, Efrat Noy wrote: Hi, I am running 2 sequential minimizations with the same mdp file. As expected the second minimization stops in step zero and the resulting structures of the 2 minimization runs are identical (RMSD=0.0). But, the energies of the last step of the first minimization (step 14) and the zero step of the second minimization are not identical (see below). What could be the reason for this mismatch? Thanks, Efrat /_First minimization_/: Step Time Lambda 14 14.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. Improper Dih. LJ-14 1.95260e+011.32951e+021.29144e+023.99233e-01 4.69282e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Pressure (bar) -3.24612e+03 -3.33371e+014.24793e+031.29742e+03 0.0e+00 _/Second minimization/_: Step Time Lambda 00.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. Improper Dih. LJ-14 2.24603e+011.31903e+021.29221e+023.98797e-01 4.61009e+01 Coulomb-14LJ (SR) Coulomb (SR) Potential Pressure (bar) -3.24585e+03 -3.32600e+014.24778e+031.29876e+03 0.0e+00 EM does a step before testing for completion.The energy terms will differ at about the 10^-1 to 10^0 kJ/mol level you are observing. However, the underlying structural differences need not be detectable in (say) a .gro file with precision in picometres. I'd expect you would see some differences with diff. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Influence of rtpi on chemical potential
Hi I am relatively new to gromacs and molecular dynamics simulations. I am trying to simulate a system of 1000 Argon atoms in an NVT ensemble in a cubic box of size 18.7886 nm(density 10kg/m^3) and temperature 90K. To do this, I have assumed that Argon interacts by Lenard-Jones(12-6) potential. My aim is to find the chemical potential. I use tpi and tpic to find this. I have performed energy minimization first and then equilibrated for a period of 1 ns(with 1 step=1fs) and then I simulate the system for 20 ns after which I do tpi/tpic on the trajectory from the 20 ns simulation. But, I noticed a thing while comparing tpi and tpic: when I increase rtpi from 1nm to 4nm, the chemical potential value changes by a factor of approximately 64(4^3),from 1 to 9 it changes by 729(9^3). I have kept nsteps = 10 and nstlist = 5. This happens for both tpi and tpic.So, am I doing something wrong here or is there any volume related normalization issue ? rtpi(nm)chemical potential 1 -0.0727196 4 -0.0009074 7 -0.0001692 Thanks Pranay Doshi -- 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] domain decomposition error
Hello Justin, I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and even 3 number of processors. I read about domain decomposition on the website and tried less number of processors, as just mentioned. My understanting after reading about the error is that parallel simulation is not working with a small system as mine! but there are 11000 atoms in there and I am doing FE stuff... I dont see why this is considered as small simulation! = There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 5.70044 nm Change the number of nodes or mdrun option -rdd or -dds = Also I checked the manual for the options below but I have no clue what value to set for my system. -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -dds real 0.8 Minimum allowed dlb scaling of the DD cell size *** Thanks, Moeed BTW: About mdp setting for electrostatics, I have set zero charges to all atoms so there is no electrostatics term ( I have only C and H). Thats why I commented out ;coulombtype = PME -- 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] domain decomposition error
Moeed wrote: Hello Justin, I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and even 3 number of processors. I read about domain decomposition on the website and tried less number of processors, as just mentioned. My understanting after reading about the error is that parallel simulation is not working with a small system as mine! but there are 11000 atoms in there and I am doing FE stuff... I dont see why this is considered as small simulation! This exact situation was just discussed last week regarding FEP and DD (hint: check the archive!). If you set your intramolecular interactions to be computed as exclusions and pairs (i.e. couple_intramol=no), then you have (essentially) long-range bonded interactions. Either use mdrun -pd or run in serial. = There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 5.70044 nm Change the number of nodes or mdrun option -rdd or -dds = Also I checked the manual for the options below but I have no clue what value to set for my system. -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -dds real 0.8 Minimum allowed dlb scaling of the DD cell size *** Thanks, Moeed BTW: About mdp setting for electrostatics, I have set zero charges to all atoms so there is no electrostatics term ( I have only C and H). Thats why I commented out ;coulombtype = PME For both solute and solvent? Just one? Seems like an unreasonable model to me. Even hydrocarbons should have some (obviously offsetting) partial charge. -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] I need ligand topology file
Hello everyone, I am using gromacs 4.5 version. I am from cadila healthcare ltd. I have protein with ligand file. But I can't submit prodrg server bcoz this confidancial data. I want to genrate .itp without using prodrg server. Have any way that i can genrate .itp file. Plz help me out. -- 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] I need ligand topology file
ajanihar...@gmail.com wrote: Hello everyone, I am using gromacs 4.5 version. I am from cadila healthcare ltd. I have protein with ligand file. But I can't submit prodrg server bcoz this confidancial data. I want to genrate .itp without using prodrg server. Have any way that i can genrate .itp file. Plz help me out. Your best resources are Chapter 5 of the manual and the primary literature for your chosen force field. There are a couple of user-contributed programs posted on the Gromacs site that will produce topologies, but nothing should supplant a proper parameterization procedure. http://www.gromacs.org/Downloads/User_contributions/Other_software http://www.gromacs.org/Documentation/How-tos/Parameterization -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] Re: angle constrain, constrained PF6 anion
Hey, Gyorgy - The problem is definitely with the incorrectly defined constraints as I mentioned yesterday. You may find Chapter 5 of the gromacs manual useful to repair this. I hope to be able to look through your attached system on the weekend, if you don't locate the problem before yourself... Regards and no runtime errors in your simulations, Vitaly On Thu, Feb 17, 2011 at 11:48 AM, gyorgy.han...@fc.up.pt wrote: Hi Vitaly, Thanks for your answer. Actually, we tried in a lot of ways to run the simulations. This was also one way, and in fact, if you use a much smaller time step, the simulation doesn't crash (I'm not saying it gives a physical result). If I remove the [bonds] part from the topology, the simulation runs and the geometry is conserved, but produces positive total energy. Maybe this is related to the unphysically high force constants of the angle bendings, but I think, this doesn't matter if the angles are contrained. (Maybe the problem is somewhere here, but I don't know how to constrain properly the angles if not like this (and nobody can tell me in my proximity)) If I remove the [angles] section, de system's total energy is negative but the geometry of the anion is completely wrong. I also have problems when running on more than 1 processor, even if I use -pd for mdrun (to switch to particle decomposition instead of domain decomposition), the simulation crashes immediately: Range checking error: Variable n has value 7. It should have been within [ 0 .. 7 ] If you want to test the topology on one single ion pair, you can find a configuration in the attachement. Thanks in advance, Best, Gyorgy Quoting Vitaly Chaban vvcha...@gmail.com: Hello, I got your files. However, the error is completely another than you mention and it occurs directly at the first time-step of the simulation. Inner product between old and new vector = 0.0! constraint #1 atoms 1377 and 1381 Wrote pdb files with previous and current coordinates step 0Inner product between old and new vector = 0.0! constraint #1 atoms 2177 and 2181 Wrote pdb files with previous and current coordinates Inner product between old and new vector = 0.0! constraint #1 atoms 2 and 6 Wrote pdb files with previous and current coordinates Segmentation fault There are a number of strange things in your configuration with the unhealthy defined constraints in topology as probably the most severe one. If you have constraints, why do you define bonds force constants at the same time? Good luck with your study, Vitaly On Wed, Feb 16, 2011 at 1:58 PM, gyorgy.han...@fc.up.pt wrote: Hi Vitaly, Thanks for your answer. I was busy with other stuff these last two weeks, that's why I have time to reply only now. So the system is the BMIM PF6 ionic liquid. We chose two potentials to describe the system, and both treat the anion as rigid. We cannot use LINCS because it shouldn't be used if one constrains not only bonds but angles too, so we have to use SHAKE. But with SHAKE I encountered some strange things as I wrote in my first thread. In the attachement I am sending you all the files needed for the simulation, maybe you'll find the problem. I havent mentioned but we try to constrain the angles by adding fictious bonds. Maybe there is something wrong with this... Thank you in advance for your help. All the best, Gyorgy Quoting Vitaly Chaban vvcha...@gmail.com: Hey Gyorgy, Your current topology file(s) is(are) also important to analyze the situation and fix the problem. Pass my kind regards to Julia... Dr. Vitaly V. Chaban, Ph.D. Department of Chemistry University of Rochester Rochester, New York 14627-0216 The United States of America = The mdp file is attached. Best, Gyorgy Quoting Justin A. Lemkul jalem...@vt.edu: gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we decided to use SHAKE. However, SHAKE seems to work a bit strangely: I know SHAKE mustn't be used with domain decomposition, but even if I set the corresponding variable to NO in the mdp file, the simulation crashes on 8 procs and gives the following error message: Fatal error: 1 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group. If I try to run mdrun with -pd (to 'really' switch off domain decomposition), the simulation doesn't chrash but gives nonsense (the energy seems to increase constantly). I am not an expert user so maybe I do something wrong but, anyway, does anyone have an
[gmx-users] Weeks Chandler Andersen potential
Hi all, I want to simulate something and want to use Weeks Chandler Andersen potential. http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential (http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential) Is table option the only way to go ? - Rohit -- 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] Weeks Chandler Andersen potential
Rohit Malshe wrote: Hi all, I want to simulate something and want to use Weeks Chandler Andersen potential. http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential Is table option the only way to go ? Buckingham and LJ are the only default van der Waals functional forms available by default. So, yes, use tables. -Justin - Rohit -- 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] saving velocities and coordinates frequently
Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? Amit -- 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] saving velocities and coordinates frequently
Amit Choubey wrote: Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? There is no such option for writing to .trr files, only .xtc files, which do not contain velocities. Implicit solvent might be an option, if appropriate for your system. -Justin Amit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: simulation of a metal binding sites
Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman ran.fried...@lnu.se wrote: Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: simulation of a metal binding sites
bharat gupta wrote: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. This list and its users should not supplant your own literature searching and learning experience. A simple Google search for: molecular dynamics metal binding yields over 60,000 results. Doubtless some of these will be useful in getting you started. There are, of course, more sophisticated literature searching tools that might serve you even better. -Justin On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman ran.fried...@lnu.se mailto:ran.fried...@lnu.se wrote: Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com mailto:bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com mailto:aanlktin06ut6%2bwrfpz4a79fq9g-galmk35uxecph%2b...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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] about -CN triple bond
Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The vsite has been mentioned, and I have refered to the gromacs manual. But I don't understand that how I can use the vsite. (add the toplogy file or use the command line?) I attach the PDB and toplogy file of the molecule. First, I performed the molecular dynamic simulation for the pure lipid bilayer, and the step was been finished. After I insert the molecule, these command lines are performed. grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr mdrun -v -deffnm em grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr nohup mdrun -v -deffnm npt_cmplx Thanks for your help. Best, Chia-yun 1.pdb Description: Protein Databank data 1.itp Description: Binary data -- 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] backbone_few_sidechain_fixed
Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows ; File 'complex.top' was generated ; By user: shahid (511) ; On host: coe.iitd.ac.in ; At date: Thu Feb 17 17:52:59 2011 ; ; This is your topology file ; They Paint Their Faces So Differently From Ours (Gogol Bordello) ; ; Include forcefield parameters #include ffG43a1.itp ; Include A-chain topologies #include complex_A.itp #include complex_B.itp #include complex_C.itp #ifdef POSRES #include posreA.itp #include posreB.itp #include posreC.itp #endif If I keep only one posreA.itp then grompp runs without error but if I use all three or two posre.itp it gives following error. Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 1275 Fatal error: [ file posreB.itp, line 118 ]: Atom index (968) in position_restraints out of bounds (1-966). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. I separated including topology and defining posres in three different parts but even then it gives error and grompp fails. In my posre.itp generated by genrestr I selected a group containing backbone and some side chains. My Idea is to keep the backbone as well as side chain of all the residues which are not on interface fixed and allow free movement of only interface residue and then run full MD. For above procedure I defined define = POSRES in full.mdp Please suggest what should I do . For a single chain I did MD keeping backbone fixed and allowing side chain free movement. In my posres.itp I used a force of 2000 kj to keep them in fixed position with option genrestr -fc. Waiting for reply Shahid Nayeem -- 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] backbone_few_sidechain_fixed
On 18/02/2011 5:14 PM, shahid nayeem wrote: Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows ; File 'complex.top' was generated ; By user: shahid (511) ; On host: coe.iitd.ac.in ; At date: Thu Feb 17 17:52:59 2011 ; ; This is your topology file ; They Paint Their Faces So Differently From Ours (Gogol Bordello) ; ; Include forcefield parameters #include ffG43a1.itp ; Include A-chain topologies #include complex_A.itp #include complex_B.itp #include complex_C.itp #ifdef POSRES #include posreA.itp #include posreB.itp #include posreC.itp #endif If I keep only one posreA.itp then grompp runs without error but if I use all three or two posre.itp it gives following error. Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 1275 Fatal error: [ file posreB.itp, line 118 ]: Atom index (968) in position_restraints out of bounds (1-966). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. grompp has told you exactly what the problem is. See http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds I separated including topology and defining posres in three different parts but even then it gives error and grompp fails. In my posre.itp generated by genrestr I selected a group containing backbone and some side chains. My Idea is to keep the backbone as well as side chain of all the residues which are not on interface fixed and allow free movement of only interface residue and then run full MD. For above procedure I defined define = POSRES in full.mdp define = -DPOSRES is the only thing with a chance of working. Mark Please suggest what should I do . For a single chain I did MD keeping backbone fixed and allowing side chain free movement. In my posres.itp I used a force of 2000 kj to keep them in fixed position with option genrestr -fc. Waiting for reply Shahid Nayeem -- 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] saving velocities and coordinates frequently
On 18/02/2011 12:21 PM, Amit Choubey wrote: Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? See www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about -CN triple bond
On 18/02/2011 1:13 PM, C.Y. Chang wrote: Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The vsite has been mentioned, and I have refered to the gromacs manual. But I don't understand that how I can use the vsite. The theory is discussed in chapter 4 and there's a brief example in 5.2.2. What have you tried and what went wrong? Mark (add the toplogy file or use the command line?) I attach the PDB and toplogy file of the molecule. First, I performed the molecular dynamic simulation for the pure lipid bilayer, and the step was been finished. After I insert the molecule, these command lines are performed. grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr mdrun -v -deffnm em grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr nohup mdrun -v -deffnm npt_cmplx Thanks for your help. Best, Chia-yun -- 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: simulation of a metal binding sites
Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental evidence for those ions being there. [1] But actually you didn't tell us which ions you want to simulate? Monovalent ions should be sort of ok, although there are differences among the forcefields (some original KCl used to crystallize). Di-valent ions, in particular Ca2+, are much more tricky. Higher charged ones are a nightmare. The higher the charge, the more likely you might want things like polarization in your simulation. There are also some specific forcefields finely parameterized for ions based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh and Piquemal. Good luck, Marc [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000 [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed) http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html bharat.85.m...@gmail.com said: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- 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: simulation of a metal binding sites
Thanks for these two references ... I am trying to simulate a zinc ion (Zn++) binding domains .. Actually the study involves grafting the Zinc ion domain onto some other protein to check whether it binds to ions or not and what will be the effect of ion binding onto the topology of the other protein to which the zinc ion binding domain is attached . On Thu, Feb 17, 2011 at 11:15 PM, Marc Baaden baa...@smplinux.de wrote: Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental evidence for those ions being there. [1] But actually you didn't tell us which ions you want to simulate? Monovalent ions should be sort of ok, although there are differences among the forcefields (some original KCl used to crystallize). Di-valent ions, in particular Ca2+, are much more tricky. Higher charged ones are a nightmare. The higher the charge, the more likely you might want things like polarization in your simulation. There are also some specific forcefields finely parameterized for ions based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh and Piquemal. Good luck, Marc [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000 [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed) http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html bharat.85.m...@gmail.com said: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.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
