[gmx-users] Simulation of the protein-ligand system embedded in membrane

James Starlight jmsstarlight at gmail.com
Thu Jul 26 15:33:12 CEST 2012


> Only if the apo form has room for you to cut and paste in all your
> ligands... You'll have to equilibrate independently in each case, so you
> don't gain anything by not creating the system from the beginning each time.

This can gain in terms of avoiding of time-consumptions solvation
phase (e.g G_membeded takes addition 50ns of simulation time )

> Have you looked in the manual and read about the options and compared the
> citations it makes to the citations of the algorithm you want to use?

I've found in manual only nh-chain-length (10) parameter wich could be
added to t_couple= Nose-Hoover.  Does the introduction of that
parameter turn on the different t_couple regime ? How I could chose
the value ( from 1 to 10) of that parameter in case of simulation of
mrmbrane proteins if I use SD integrator ( not MD). Does any other
integrator could be most suitable for chains regime ?


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