[gmx-users] coarse-grained model

Yang Ye leafyoung81-group at yahoo.com
Wed Jul 12 05:18:50 CEST 2006


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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>>
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