[gmx-users] EM error

[Justin Lemkul]

On 1/9/13 8:42 PM, Xu Dong Huang wrote:
> Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD< it's certainly not overlapping with my solute. )
>

It seems like all the waters are being placed too close to the polymer beads, so 
you should probably increase the value of -vdwd when running genbox.  You can 
make your life easier in visualization by selecting only certain atoms to 
display, i.e. by using the Tk console:

set myatoms [atomselect 0 "(within 5 of index 14523)"]
animate write pdb myfile.pdb sel $myatoms

That saves the coordinates of any atom within 5 Angstrom of the problematic atom 
below (14524, or index 14523).  Displaying these atoms only can be much more 
useful than trying to sift through 70000+ atoms.

-Justin

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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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