[gmx-users] Dynamics of the salt-bridges

[Erik Marklund]

Hi,

If you don't care about the exact distances, but rather the time the  
groups spend within a certain distance, g_hbond -contact can be useful.

Best,
Erik

On Feb 3, 2013, at 6:36 PM, James Starlight wrote:

> 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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