Re: [gmx-users] Re: Gromacs analysis tools for Namd output
--- On Tue, 7/2/12, Kunze, Micha micha.kunze...@ucl.ac.uk wrote: cant help you with the plugin issue, but have you instead tried loading the dcd trajectory into vmd and save it as trr? No need to open it with VMD. You can use catdcd (http://www.ks.uiuc.edu/Development/MDTools/catdcd/) to do the conversion: catdcd -o output.trr -otype trr input.dcd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to assign charge group codes to atoms of new residue -Regd
Dear Gromacs users, As i am planning to use Gromacs for simulations of my system consisting of CH3-CH2-O, and as the CH3-CH2-O residue parameters are not available by default in charmm27.ff, so i am trying to add the parmeters of this residue to charmm27.ff,but struck where i am not sure how to assign charge group codes which will be denoting the charge group numbers for the atoms of this residue in .rtp file.Is there any procedure that has to be followed to assign particular values as charge group codes. Any help will be highly appreciated. Thank you Regards, Ramesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to assign charge group codes to atoms of new residue -Regd
On 9/02/2012 6:05 AM, ramesh cheerla wrote: Dear Gromacs users, As i am planning to use Gromacs for simulations of my system consisting of CH3-CH2-O, and as the CH3-CH2-O residue parameters are not available by default in charmm27.ff, so i am trying to add the parmeters of this residue to charmm27.ff,but struck where i am not sure how to assign charge group codes which will be denoting the charge group numbers for the atoms of this residue in .rtp file.Is there any procedure that has to be followed to assign particular values as charge group codes. One atom per charge group. There's discussion of this issue in the mailing list archives. 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] g_x2top
Hi, I am running Gromacs 4.5.5. I am using a colleague's homemade forcefield, and I am trying to use g_x2top to generate a .top topology file from a .gro configuration file. This should be possible, because my colleague's forcefield contains a file to translate atom names into atom types (a .n2t library file). My configuration file is called conf.gro. I run g_x2top using the command: g_x2top -f conf.gro -o out.top -ff select The program prompts me for a forcefield, and I choose my colleague's forcefield, which is located in my working directory. g_x2top runs for a few minutes and ultimately gives this error message: --- Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 7147 out of 7216 atoms --- g_x2top also gives me many other error messages of the form (I get 69 such messages, where 69 is exactly the number of atoms for which g_x2top could not find a forcefield type): Can not find forcefield for atom X-INDEX with # bonds where X is an atom name, INDEX is that atom's index in conf.gro, and # is the number of bonds. For example, one of these error messages is Can not find forcefield for atom B0-6067 with 3 bonds, and I am wondering if you can please give me advice on this. B0 is indeed an atom name (for boron) and in conf.gro, atom 6067 is indeed B0. However, my conf.gro is written such that B0 6067 is surrounded by four fluorine atoms, since the residue is the anion boron trifluoride (BF4-): 287BF4 B0 6067 1.302 2.728 16.210 0.0905 0.7350 -1.6601 287BF4 F1 6068 1.237 2.622 16.271 0.3710 -0.9520 0.6277 287BF4 F2 6069 1.267 2.739 16.082 0.9097 -0.5184 -0.3121 287BF4 F3 6070 1.425 2.712 16.219 0.2955 -0.5337 -0.0541 287BF4 F4 6071 1.262 2.846 16.270 0.6101 -0.5227 0.5296 where the boron-fluorine bond lengths here are 0.138499 nm, 0.133154 nm, 0.124362 nm, and 0.13829 nm, respectively. My colleague's .n2t file contains the following line (among many others): B0 B 1.1504 10.8100 4 F1 0.1390 F2 0.1390 F3 0.1390 F4 0.1390 which means, I think, that g_x2top expects each boron atom to be surrounded by four fluorine atoms with the bond length 0.1390 nm. My question is, why does g_x2top think that boron B0-6067 is bonded to only 3 atoms: Can not find forcefield for atom B0-6067 with 3 bonds? Is it that the B0-F3 bond length (0.124362 nm) in conf.gro is just too far from the bond length that it expects (0.1390 nm)? Is there any way to get around this, to tell g_x2top to be more liberal in accepting bonds? (Probably not, because in http://manual.gromacs.org/current/online/x2top.html I do not see any options to modify this, and I understand that the atom selection is primitive.) The problem is, I guess, that the conf.gro that I have is not a starting configuration; it is from some frame during my colleague's simulation, when bonds were stretched and compressed, etc. Do you have any advice whereby I could still use this non-starting configuration? Thanks so much. 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] LINCS warning and segmentation fault for methane in 1-octanol simulation
Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. Regards, Vivek Sharma -- 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
