On 9/4/12 11:59 AM, [email protected] wrote:
Yes okey. I understood.
But I have another question:
Since I only want to minimize the phosphates which I added to the protein
I want to use the freeze option to make sure that the other residues will
not change.
But how can I say gromacs that it shell make an exception and do not
freeze the phosphate of the residues where I added the phosphate?
Use the freezegrps option in the .mdp file, along with suitable index groups.
-Justin
Thank you,
Eva
Only the -ignh flag is wrong, as Justin said.
Keep the rest of the command line.
--
Marcelo Depólo
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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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