[gmx-users] Switching off electorstaic
samrucu at yahoo.co.in
Wed Oct 11 08:45:35 CEST 2017
Thanks a lot. It seems much more reasonable. Let me try with the free energy code. And, yes, I understand that the system will not behave as a physical system. I just want to check the effect of charged residues on the polymer properties of the chain.
On Sunday, 8 October 2017 2:01 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On 08/10/17 04:12, atanu das wrote:
> I am intending to run a simulation of a protein in 100 nM NaCl solution by turning off protein's electrostatic interactions, but keeping the LJ alive, so that water and salt behave as usual and the protein only behaves as a hydrophobic polymer chain. The most obvious way that I could think of is editing the topol.top file and setting the partial charges of all the protein atoms to be zero. However, I am slightly skeptical about using such a crude method. Is there any better way to turn off the electrostatics of the protein only?
You may want to slowly turn of the charges using free energy code
although it will be slower. Of course even a hydrophobic chain has
charges, and doing what you plan to will mess up the balance between
Coulomb and Lennard-Jones interaction. You may get some insight but
nothing of physical relevance that you can compare to any experiment.
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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