[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 15 23:54:09 CET 2011

Алексей Раевский wrote:
> Hi, I have got a situation and I don't know how to cope with it. I 
> carried out a simulation in gromacs 4.5.3 and the objects are protein, 
> rna, water...The idea is that one atom part of rna has to create an 
> h-bond with a water molecule, which at the same time makes h-bonds with 
> aminoacids of the binding site. Something like a coordination molecule. 
> So a command g_dist with index file and distance 0.35 showed me a number 
> of water molecule I needed. But when I decided to visualize this process 
> I saw that my protein with rna  went out from the water box to another 
> "cell" and the part of rna sppeared in the bottom of this box (( as I 
> know this is not a bug or error of pbc. But i don't understand what is 
> happening. Does my water forms bonds with this part and aminoacids (!!!) 
> of binding site, because when I've converted trr to pdb with index file 
> (atoms of binding site, part of rna, water molecules I've got with 
> g_dist) I saw water molecules with part of rna in the bottom of display 
> and binding site in the top...I tried to use -pbc nojump and center, 
> -pbc mol...this flags united protein, rna and part of rna togetrher, but 
> my water is not there (((( Thank you

For proper visualization, there is a workflow here:


For complex systems, multiple iterations of trjconv are almost certainly 
required, some or all of which might need custom index groups.

Bridging and simultaneous hydrogen bonds have been discussed frequently in the 
last few weeks.  Have a look through the list archive.  g_dist and g_hbond are 
the proper tools, but multiple operations and your own post-processing of such 
data will be required to extract the information you need.



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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