Hi
I have been trying to optimize well-tempered metadynamics simulation in Gromacs 2020.4 engine using plumed, on a transporter from Major Facilitator Superfamily. I have the existing structure in outward facing (OF) conformation, and want to address the inward facing (IF) conformation. For this I equilibrated the transporter in POPE bilayer as it facilitates OF to IF transition. The system was equilibrated at 310K and I am using the following plumed.dat file for running metadynamics with temp=323K:
# vim:ft=plumed
MOLINFO STRUCTURE=reference.pdb
# angle between N-terminal extracellular portion (ne), C-terminal extracellular portion (ce) and C-terminal cytoplasmic portion (cc) are taken as CV. So, angle ne-ce-cc is acute in OF conformation and obtuse in IF conformation.
ne: COM ATOMS=
Hi Wojciech Kopec
We don't know the energy dependency, but from the structure that we solved, it seems like a proton coupled transporter. I will try to find approx. harnessable energy through nernst potential, although I am skeptic that it would yield this much energy. Thanks anyways!
Hi
I got the answer, I think, as an explanation given here:
https://www.plumed.org/doc-v2.6/user-doc/html/_r_e_w_e_i_g_h_t__m_e_t_a_d.html
Bascially, when there is a metadynamics bias acting on a CV, the bias will have an effect on the region of phase space that will be sampled when an MD simulation is run using this variable. Consequently, when the histogram as a function of the CV, (in this case, the angle a1) is accumulated, we have to use reweighting into order to discount the effect of the bias from our final histogram. We do not use REWEIGHT_BIAS here, however, as the bias changes with time. We thus use the reweighting algorithm for metadynamics instead.
Thanks Wojciech Kopec
for your input!- Badges
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