[gmx-users] about tabulated potentials

[Liu, Liang]

Thanks, I will try to figure it out.

On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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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-- 
Best,
Liang Liu
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