[gmx-users] LINCS warning in md run

Justin Lemkul jalemkul at vt.edu
Thu Sep 13 11:53:21 CEST 2012

On 9/13/12 5:50 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Ah okey. Thank you.
> I will write them.
> Hmm, but the protein is a crystal structure from pdb with a resolution of
> 1.2. I already added the hydrogen atoms to this structure and there I
> already minimized them and made a md run. And there were no errors. And
> now I only added the phosphate to the minimized structure. So I thought
> that I only had to minimize the phosphate and the residue it bound on.
> Or is there a mistake in my thought here?

If adding the phosphate resulted in a crash, then clearly that's the problem.  I 
don't understand why you would run EM on just the phosphate and keep the rest of 
the protein structure frozen.  Again, that potentially prevents clashes from 
being resolved.  I don't understand what value there is in only minimizing the 



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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