<font color="#000099"><font face="verdana,sans-serif">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.</font></font><div>
<font color="#000099"><font face="verdana,sans-serif">The procedure I apply is as following:</font></font></div><div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif"><div>
pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce</div><div>editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0</div><div>genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top</div><div>grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2</div>
<div>mdrun -v -s em.tpr -c em.pdb -table table.xvg</div><div><br></div><div>And the em.mdp file is:</div><div><div>cpp = /usr/bin/cpp ; Preprocessor</div><div>include = -I../top ; Directories to include in the topology format</div>
<div>define = -DFLEX_SPC</div><div>integrator = steep ; Algorithm options</div><div>dt = 0.002 ; ps ! ; run control, the time step</div><div>nsteps = 1000 ; run steps, simulation length = dt*nsteps</div>
<div>nstenergy = 10 ; Write energies to disk every nstenergy steps</div><div>nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps</div><div>xtc_grps = RNA ; Which coordinate group(s) to write to disk</div>
<div>energygrps = RNA ; Whici energy group(s) to write to disk</div><div>nstlist = 10 ; Frequency to update the neighbor list and long range forces</div><div>
ns_type = grid ; Method to determine neighbor list and long range forces (simple, grid)</div><div>rlist = 1.0 ; Cut-off for making neighbor list (short range forces)</div>
<div>vdw-type = user</div><div>coulombtype = user ; Treatment of long range electrostatic interactions</div><div>rcoulomb = 1.0 ; long range electrostatic cut-off</div>
<div>rvdw = 1.0 ; long range Van der Walls cut-off</div><div>constraints = none</div><div>pbc = xyz</div><div>emtol = 5000.0</div><div>emstep = 0.01</div>
</div></font></font><div><br></div><div>All the procedure and file are right? Thanks.</div><div><br></div>-- <br>Best,<br>Liang Liu<br>
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