[gmx-users] NVT equilibration of ethanol in OPLSAA ff
Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I scaled the solvent box for the density of ethanol (785.22 g/l) at 298.15. Before creatin solvent box I EM the isolated solvent molecule, then I used that molecule to generate the solvent box. Then I EM the solvent box 512 molecules.Followin are the parameters for EM of Solvent box. ; RUN CONTROL PARAMETERS integrator = steep ; start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1 nstlist = 10 rlist= 1.1 coulombtype = pme pme_order= 4 fourierspacing = 0.16 rcoulomb = 1.1 vdw-type = cut-off rvdw = 1.1 nstenergy= 10 ; ENERGY MINIMIZATION OPTIONS emtol= 1000.0 emstep = 0.1 I saw the em.xvg file it is minimized well. Then I started NVT equilibration with lincs constraints for hbonds at timesteps of 0.2 fs and runned for 5 ps. The resultant configuration shows that most of the molecules were together at region of box and there was some void inside the box. I used cut-off of 1.1 nm for electrostatic and VdW interactions. I didn't use any shift or switch function. (can anybody suggest me a good tutorial to understand the judicious use of this functions.) Please help me sort this problem. If you need further details I am ready to send you. Thank you. With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, 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/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] angke definition
Hi, i need your help again! this time in the selection of analyzing tools and methods... I've found a water molecule near one of the ligand atoms. It's stabile enough and the distance is about 3.3 A. But I want to make some measurments, exactly angle degree identification. I want to calculate the frequence of forming of angle (about 90 degree) between oxygen of the water and the plane (formed by the atom of the ligand and several atoms around (it is a first CA atom and carboxyl group CA-C-O-OH of aminoacid)). But a perpendicular from OW is connected exactly to C atom of carboxyl group. In other case gromacs is trying to calculate an angle between OW and the whole, unlimited plane... Can I do such analyze? Ormay be you can give me some advices Thank you! -- * Nemo me impune lacessit* -- 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] NVT equilibration of ethanol in OPLSAA ff
On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote: Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I scaled the solvent box for the density of ethanol (785.22 g/l) at 298.15. Did you view the system+box at this stage? What were your actual commands? You will get much more effective help if you provide an excess of information, than if you expect people to guess the right follow-up questions when they have little information. Before creatin solvent box I EM the isolated solvent molecule, then I used that molecule to generate the solvent box. Then I EM the solvent box 512 molecules.Followin are the parameters for EM of Solvent box. ; RUN CONTROL PARAMETERS integrator = steep ; start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1 nstlist = 10 rlist= 1.1 coulombtype = pme pme_order= 4 fourierspacing = 0.16 rcoulomb = 1.1 vdw-type = cut-off rvdw = 1.1 nstenergy= 10 ; ENERGY MINIMIZATION OPTIONS emtol= 1000.0 emstep = 0.1 I saw the em.xvg file it is minimized well. Then I started NVT equilibration with lincs constraints for hbonds at timesteps of 0.2 fs and runned for 5 ps. The resultant configuration shows that most of the molecules were together at region of box and there was some void inside the box. I used cut-off of 1.1 nm for electrostatic and VdW interactions. I didn't use any shift or switch function. (can anybody suggest me a good tutorial to understand the judicious use of this functions.) What you've done is fine so far. There is no clear path for these choices. Ideally you should consider the scheme under which the force field was parameterized, and how it has been successfully used since, and do something very similar. Mark Please help me sort this problem. If you need further details I am ready to send you. Thank you. With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, 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/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] angke definition
Hey :) Would g_sgangle be capable of what you want? Otherwise, your best bet seems to be writing the atoms involved to an easily readable format (.gro/.pdb) and do the math in Python. I can send you a backbone Python script for reading .gro/.pdb trajectories if you want. Cheers, Tsjerk On Wed, Oct 5, 2011 at 10:08 AM, Алексей Раевский rayevsk...@gmail.com wrote: Hi, i need your help again! this time in the selection of analyzing tools and methods... I've found a water molecule near one of the ligand atoms. It's stabile enough and the distance is about 3.3 A. But I want to make some measurments, exactly angle degree identification. I want to calculate the frequence of forming of angle (about 90 degree) between oxygen of the water and the plane (formed by the atom of the ligand and several atoms around (it is a first CA atom and carboxyl group CA-C-O-OH of aminoacid)). But a perpendicular from OW is connected exactly to C atom of carboxyl group. In other case gromacs is trying to calculate an angle between OW and the whole, unlimited plane... Can I do such analyze? Ormay be you can give me some advices Thank you! -- Nemo me impune lacessit -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] angke definition
On 5/10/2011 7:28 PM, Tsjerk Wassenaar wrote: Hey :) Would g_sgangle be capable of what you want? Otherwise, your best bet seems to be writing the atoms involved to an easily readable format (.gro/.pdb) and do the math in Python. I can send you a backbone Python script for reading .gro/.pdb trajectories if you want. Or g_traj -xvg none and a scripting language of choice. Mark Cheers, Tsjerk On Wed, Oct 5, 2011 at 10:08 AM, Алексей Раевскийrayevsk...@gmail.com wrote: Hi, i need your help again! this time in the selection of analyzing tools and methods... I've found a water molecule near one of the ligand atoms. It's stabile enough and the distance is about 3.3 A. But I want to make some measurments, exactly angle degree identification. I want to calculate the frequence of forming of angle (about 90 degree) between oxygen of the water and the plane (formed by the atom of the ligand and several atoms around (it is a first CA atom and carboxyl group CA-C-O-OH of aminoacid)). But a perpendicular from OW is connected exactly to C atom of carboxyl group. In other case gromacs is trying to calculate an angle between OW and the whole, unlimited plane... Can I do such analyze? Ormay be you can give me some advices Thank you! -- Nemo me impune lacessit -- 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] NVT equilibration.
Dear All, My commands where, genconf_d -f ethanol.gro -o ethanol512.gro -nbox 8 8 8 editconf_d -f eth512.gro -density 785.22 -o den.gro I saw the den.gro by using VMD. I saw only as points but not the molecules. EM: grompp_d -f em.mdp -c den.gro -p ethanol.top -o em.tpr mdrun_d -deffnm em I saw em.gro using VMD. Now I see ethanol molecules arranged all over thebox in order. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] protein_model_refinement
Dear All I am trying to refine a protein model which is a homodimer with each chain having 609 residues.I tried minimizing in Chimera and then checking models with procheck.Infact model quality deteriorated as far as Ramachandran plot is concerned. Will doing MD simulation help me in Gromacs. It is a big protein so long MD simulation is not possible. Short duration MD will be insufficient to search native structure. I am stuck-up. Can anyone on this list help me. 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
[gmx-users] RE:Data Analysis
Dear All, I woundered if anyone has scripts/tools or suggestions for analyzing energy changes from extracted run data. Mostly I end up with 20 spread sheet columns for a large system with 2x2 domain proteins, a peptide of 10-20 amino acids and soome small molecules. I've been playing with the data via xmgrace and qtiplot, and using formulas by hand via liturature. I am also breaking things down into simplified energy runs (EQ via NPT 50 ps, then a simple MD for 2-5 picosecounds with the systems components seperated in solvent, and the system components in a complex in solvent. Then extended runs for one or two systems that look nice for different (structural and interaction based) analysis. Mostly though I just woundered if anyone had scripts (Python, java, C++, etc...) for manipulation the extracted energy data and producing an output column for totals, or a summed single number output for varied energy components. Mostly I found the Gromacs normal data manipulation (g_lie) works well with small molecules for a simple quick EQd run, but not for large proteins, etc... Sincerely, Stephan Lloyd Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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] dihedral restraints documentation
Just a note concerning dihedral restraints documentation -- the function and default behavior of dihre-fc needs to be documented somewhere in the manual. I just spent a couple hours (and my student a couple of days!) trying to track down the source of some crashes which ended up being due to the difference between specifying dihre-fc = 1 in our topology file, and not specifying anything at all. THis how-to documents what dihre-fc DOES ( http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints) but it is not mentioned anywhere in the gromacs manual at all. It turns out dihre-fc defaults to 1000, so the difference between dihre-fc = 1 and omitting dihre-fc is a factor of 1000 in dihedral restraint strength. This is enough (since it's a multiplier!) to make the difference between simulations reliably crashing and simulations not crashing at all... This clearly should be documented in the manual since (with this behavior) knowing what value of dihre-fc one is using is critical to knowing what dihedral restraint strength one is using. Thanks. -- David Mobley dmob...@gmail.com 504-383-3662 -- 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: NVT EQUILIBRATION
Keep the discussion to the emailing list please. How many molecules that is required you can calculate yourself. What is the density? You know the volume, therefore you can calculate yourself how many molecules should be in that space, simple calculation. You should also be able to eye ball based on the coordinate file you mentioned that was full of voids. If the voids take up about half of the box, you need roughly double the number of molecules, quarter, then you need 33% more. Plus, you can do it via trial and error, but the density calculation is the way to go. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: Ravi Kumar Venkatraman [mailto:ravikumarvenkatra...@gmail.com] Sent: Wednesday, 5 October 2011 7:48 PM To: Dallas Warren Subject: NVT EQUILIBRATION Dear Dallas Warren, Yes you are right. Pressure was going negative when I did NPT equilibration. So increasing # of molecules will help me. If at all tell me how many molecules I should have approximately. Thank you for your help. With Regards, Ravi Kumar Venkatraman. -- 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] Protein_model_refinement
Dear All I want to refine a protein homology model, I did minimization but then procheck does not give better Ramachandran plot. This model is a homodimer with each chain of 609 residue and a total of 1218 residue so a long MD simulation to search native state is not feasible. Can any one help me on this list to tell that how should I attempt this problem. 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
