[gmx-users] about tabulated potentials

[Sikandar Mashayak]

>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 <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 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
>
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