[gmx-users] about tabulated potentials

[Liu, Liang]

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.
>
> 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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>
>
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-- 
Best,
Liang Liu
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