[gmx-users] about tabulated potentials

[Mark Abraham]

On 16/11/2011 2:45 PM, Liu, Liang wrote:
> 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?

See manual sections 7.3.12 and 6.7.2.

> And how to generate the index file? I am sorry for so many questions, 
> I am really not familiar with it.

http://www.gromacs.org/Documentation/File_Formats/Index_File

Mark

>
> On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak 
> <symashayak at gmail.com <mailto: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
>     <mailto: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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>
>
> -- 
> Best,
> Liang Liu
>
>

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