[gmx-users] Re: water dimer is gas phase

Justin A. Lemkul jalemkul at vt.edu
Fri May 20 17:08:05 CEST 2011

Nilesh Dhumal wrote:
> I run the same mdp files for glucose in vaccum.
> I ma geting the proper results, I can visualize the strucutre properly in
> VMD.
> If I use same for water why I am not geting proper structure ?

You're comparing dissimilar systems and expecting them to somehow behave the 
same way.  I would suspect that your water dimer simply flies apart.  There's 
nothing "wrong," per se, with this outcome, but large coordinate values break 
the required PDB formatting.  I believe this is what Erik was getting at - you 
can process the .pdb file to conform to proper spacing.  Presumably there are 
usable frames in your .trr/.xtc file that you can watch to see what's happening 
in the simulation, but I suspect that you'll find the water molecules are simply 
drifting apart.



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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