Thanks, I will try to figure it out. On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 16/11/2011 2:45 PM, Liu, Liang wrote: > > Thanks for help. > If I have more atoms and they can interact each other or itself, like PP, > PC, PN, CP, CN, CC .... How's the energygrp_table looking like? > I know there should be a option in the grompp, but how to do that? > > > See manual sections 7.3.12 and 6.7.2. > > > And how to generate the index file? I am sorry for so many questions, I > am really not familiar with it. > > > http://www.gromacs.org/Documentation/File_Formats/Index_File > > Mark > > > > On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak > <symasha...@gmail.com>wrote: > >> >From your system information, I understand that you need to specify >> tabulated potentials between atoms P and P, and between atoms C and P, and >> so on. >> >> To achieve this, you need to create energy groups with atom types P and >> C, and specify energygrp_table options in the grompp such as following >> >> .... >> >> energygrps = P C ; (and rest of the groups in your system, you will need >> to specify index file containing energy groups ) >> energygrp_table = P P P C >> >> .... >> >> so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run >> directory, and uses it for P-P and P-C interactions, whereas for all other >> interactions default table.xvg file is used. >> >> >> I hope this helps. >> >> Regards >> Sikandar >> >> >> On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang <liu4...@gmail.com> wrote: >> >>> I am trying to use a serial of tabulated potentials, which are the >>> functions of the distance between atoms and the names are table.xvg, >>> table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some >>> RNA structures. >>> The procedure I apply is as following: >>> >>> pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce >>> editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 >>> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top >>> grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 >>> mdrun -v -s em.tpr -c em.pdb -table table.xvg >>> >>> And the em.mdp file is: >>> cpp = /usr/bin/cpp ; Preprocessor >>> include = -I../top ; Directories to include >>> in the topology format >>> define = -DFLEX_SPC >>> integrator = steep ; Algorithm options >>> dt = 0.002 ; ps ! ; run control, the time >>> step >>> nsteps = 1000 ; run steps, simulation >>> length = dt*nsteps >>> nstenergy = 10 ; Write energies to disk >>> every nstenergy steps >>> nstxtcout = 10 ; Write coordinates to >>> disk every nstxtcout steps >>> xtc_grps = RNA ; Which coordinate >>> group(s) to write to disk >>> energygrps = RNA ; Whici energy group(s) >>> to write to disk >>> nstlist = 10 ; Frequency to update the >>> neighbor list and long range forces >>> ns_type = grid ; Method to determine >>> neighbor list and long range forces (simple, grid) >>> rlist = 1.0 ; Cut-off for making >>> neighbor list (short range forces) >>> vdw-type = user >>> coulombtype = user ; Treatment of long range >>> electrostatic interactions >>> rcoulomb = 1.0 ; long range >>> electrostatic cut-off >>> rvdw = 1.0 ; long range Van der >>> Walls cut-off >>> constraints = none >>> pbc = xyz >>> emtol = 5000.0 >>> emstep = 0.01 >>> >>> All the procedure and file are right? Thanks. >>> >>> -- >>> Best, >>> Liang Liu >>> >>> -- >>> 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 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 >> > > > > -- > Best, > Liang Liu > > > > > -- > 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 > -- Best, Liang Liu
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