[gmx-users] about tabulated potentials

Liu, Liang liu4gre at gmail.com
Tue Nov 15 21:49:26 CET 2011

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
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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