[gmx-users] about tabulated potentials
liu4gre at gmail.com
Wed Nov 16 04:45:45 CET 2011
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? And how
to generate the index file? I am sorry for so many questions, I am really
not familiar with it.
On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak <symashayak at 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.
> On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang <liu4gre at 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
>> 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
>> rvdw = 1.0 ; long range Van der Walls
>> constraints = none
>> pbc = xyz
>> emtol = 5000.0
>> emstep = 0.01
>> All the procedure and file are right? Thanks.
>> Liang Liu
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