[gmx-users] Dynamics of the salt-bridges

Justin Lemkul jalemkul at vt.edu
Sun Feb 3 18:06:06 CET 2013

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


> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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