SanDisk Membrain Software Uživatelský manuál stáhnout pdf (Strana 39)

3 RUNNING A SIMULATION OF KCSA 39

Warning. The conﬁguration ﬁles provided in this tutorial are de-

signed for users with limited computational resources. Thus, simu-

lations are performed using a 2 fs timestep, the SHAKE algorithm

for hydrogen atoms, and a multiple time stepping algorithm for the

computation of long-range electrostatic interactions. Ideally, one

should use a uniform 1 fs time step without SHAKE. This is partic-

ularly important for long simulations performed at constant energy.

However, you may want to still keep water molecules rigid, as the

CHARMM force ﬁeld was parameterized using rigid water molecules.

19 Once your simulation is done, open VMD and load the trajec tory

kcsa popcwimineq-01.dcd on top of the corresponding PSF ﬁle

kcsa popcwi.psf.

If your simulation was successful, lipid tails should now look disordered (Fig. 12).

3.2 Minimization and Equilibration with Protein Constrained

We are not quite ready for running the system with full dynamics. Be cause we

have put our system together by hand, it has many unnatural atomic positions.

If we tried to do a dynamics run now, it would immediately fail, with many

atoms moving at very high velocity. Thus, our second run with NAMD will

be a “minimization” run, which simply guides the system to the nearest lo cal

energy minimum in conﬁguration space. Minimization will be then followed by

an equilibration with the protein constrained, so as to permit the environment

to relax ﬁrst.

1 Set your current directory to mem-tutorial-files/03-MINEQ/

2 Open the ﬁle kcsa popcwimineq-02.conf in a text e ditor.

3 Check that the outputName has been changed appropriately.

4 Go to the section # Continuing a job from the restart files:

# Continuing a job from the restart files

if {1} {

set inputname kcsa_popcwimineq-01

binCoordinates $inputname.restart.coor

binVelocities $inputname.restart.vel

extendedSystem $inputname.restart.xsc

}

firsttimestep 251000

Note how we have activated this section (“if{1} {” instead of “if{0} {”) so

NAMD can read the restart ﬁles from the previous run. The counter of time

steps has also been updated.

1 2 ... 34 35 36 37 38 39 40 41 42 43

Žádné komentáře

SanDisk Membrain Software Uživatelský manuál Strana 39