[gmx-users] Dynamics of the salt-bridges

[James Starlight]

Justin,

1 )for example I want to select in index file only all asp, glu and
his residues ( I could find selection by residue type only).

2) Than I'd like that gromacs compute dynamics of the distance between
that charge groups (providing only truncated .tpr file as the input)
but only. Could other than g_saltbr gromacs tools be used for that
(E,g g_dist ) ?


James

2013/2/3 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 2/3/13 1:01 AM, James Starlight wrote:
>>
>> Justin,
>>
>> thanks again for suggestions.
>>
>> I'm not quite sure how I can use tpbconv -zeroq. For example I want to
>> reduce charges of all amino acids except Asp Glu and His ( to monitor
>> s.b dynamics between that groups only).
>>
>> As I understood -zeroq working with the groups defined in the index
>> file so I should just  select all residues that I need in that file,
>> shouldnt it  ? Also doest it possible to select pairs of residues
>
>
> Yes.
>
>
>> placed in the sequence on the distant sites ? (e.g by selecting only
>> pairs within some range of n1 and n2+k where k>n1+10)
>>
>
> I don't understand what you mean.  tpbconv will only take one index group
> for zeroing charges, so I don't understand how such a relative scheme would
> work for all cases.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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