[gmx-users] reg g_morph

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 9 16:50:27 CEST 2011

vidhya sankar wrote:
> Dear justin,
>                    Thank you for your previous patient reply
> When i use  trjconv tool using -b & -e option i have got the number of 
> intermediate structures. for the selected time interval
>  i have used the  pdb of first and last (obtained throug trjconv)  in 
> g_morph tools to get linearly interpolated structure . there also i have 
> got 23 different linearly interpolated structure  can i compare these 
> two set of pdb (obtained through trjconv and g_morph tools) . 
> will the time factor  match ?  .because  g_morph shows time factor 
> according to -ninterm flags which is actually different from actual .trr 
> files obtained through Dynamics. is it possiblie to compare.
> also g_morph tool does not take ant time as input. .but .xvg file 
> (output) shows time factor. as one of variable
> I am eagerly expecting your reply.
> Thanks in advance

I doubt there is any relationship between the structures extracted by trjconv 
and those produced by g_morph, since the structures from dynamics will be those 
produced by the actual forces in the simulation and the structures from g_morph 
will be unphysical intermediates based on simple linear interpolation.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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