Skip to main content

Table 3 Thermalization scheme of the two simulated systems.

From: Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant

Time (ps)

Thermalization phases

Steps number and Δt

Position restraint (kcal/mol·Å)

0

EM 1

10000

500

0

EM 2

20000

500

12.5

MD 1

25000 – 0.5 fs

500

0

EM 3

15000

25

25.0

MD 2

25000 – 1.0 fs

25

0

EM 4

10000

-

20.0

MD 3

10000 – 2.0 fs

-

40.0

MD 4

20000 – 2.0 fs

-

100.0

MD 5

50000 – 2.0 fs

-

  1. The execution time is reported in the left column. EM indicates an Energy Minimization procedure and MD a Molecular Dynamics procedure. For the initial thermalization steps, evidenced in bold, the values of position restraints are shown in the last column.