[gmx-users] About g_mdmat function

[Keunwan Park]

Thank you for the suggestion !

Originally, there were about 250 residues.
"182 residues" might be from the end-index of
'r_81_r_82_r_83_r_102_r_111_r_149_r_178_r_182' .

Do I make wrong index file ? or, is the result-file normal?


Keunwan Park


Mark Abraham wrote:
> Keunwan Park wrote:
>   
>> Dear all
>>
>> I use index file to make residue group and run g_mdmat function with the
>> ndx file.
>>
>> For example, the residue groups are composed of 8 residues and the
>> program said ...
>> --------------------------------------------------------------------------
>> Selected 10: 'r_81_r_82_r_83_r_102_r_111_r_149_r_178_r_182'
>> There are 182 residues with 100 atoms
>> --------------------------------------------------------------------------
>>
>> Why the program recognize 182 as a total residue number instead of 8 ?
>> PixMap matrix file also show 182 residues.
>>     
>
> Were there 182 residues originally?
>
>   
>> How do I draw the matrix file with 8 residues ?
>>     
>
> You can use modes of trjconv and tpbconv to make trajectory and run
> input files for only this subset of the residues and give those as input
> to g_mdmat.
>
> Mark
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