[gmx-users] coarse-grained model

[Dongsheng Zhang]

Yang Ye,

I am sorry to tell you I am not clear yet. Do you think I need to
specify energygrps and corresponding energygrp_table? 

If so, then I got any error message. gp1 includes atom A, and gp3
includes atom A and B. Gromacs will complain that atoma has been in two
groups. Each group uses it own different table, but the group members
are overlapping bwteen some groups. How can I fix it?


If not, I really have concern how gromacs knows to look for
table_A_A.xvg when it calculates A-A nonbonded interaction and look for
table_A14_A14.xvg when it calculates 1-4 interaction between A and A
monomers. 

Could you please give me more instruction? Thank you for your help!


Dongsheng


On Wed, 2006-07-12 at 11:18 +0800, Yang Ye wrote:
> Don't worry about that.
> mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg, 
> {tablep}_B_B.xvg ...
> {tablep} may be replaced by your own filename.
> 
> Yang Ye
> 
> Dongsheng Zhang wrote:
> > Yang ye,
> >
> > Thank you very much.
> >
> > I have three different monomers in my system, so I have 6 different
> > regular VMDs and 6 different 1-4 interactions. Could you please tell me
> > how to organize those table.xvg files?
> >
> > energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
> > energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
> > B14 A14 C14 B14 C14 
> >
> > If I set as the above, I wonder how gromacs know the last 6 table is for
> > 1-4 interaction.
> >
> > All the best!
> >
> > Dongsheng
> >
> > On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote:
> >   
> >> mdrun -tablep
> >>
> >> Dongsheng Zhang wrote:
> >>     
> >>> Hello, GMX users,
> >>>
> >>> I have a coarse-grained model. Both 1-4 and regular vdw interaction are
> >>> tabulated, but no electrostatic interaction. Since there is no entry for
> >>> 1-4 interaction in energy_table. I am thinking to fool gromacs by
> >>> treating 1-4 interactions as electrostatic interactions, in other words,
> >>> every time when 1-4 interaction energy needed, I will ask gromacs to
> >>> calculate COUL energy by reading energy_table. Does anyone know where
> >>> 1-4 interaction is calculated and how I can switch it to calculate COUL
> >>> energy in the source code? Any help will be highly appreciated!
> >>>
> >>>
> >>> All the best!
> >>>
> >>>
> >>> Dongsheng
> >>> _______________________________________________
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