How to run a complete simulation

Theory

The .pdb is generated from X-ray diffraction crystallography. This process requires a crystal of the protein, which occurs only at low temperature (~5°K). Taking this in consideration, we have to go through different steps to bring our protein to lab conditions. Please refer to the page on .conf parameters to see how to perform these steps in namd.

Initial minimization

We start with a few minimization rounds, to reach a minimum in the sense of potential energy.

Heating

When the protein is stable, we have to add heat (kinetic energy) to reach a higher temperature (~300°K). We have to take a special care not to add heat too fast, which would result in protein burst and explosion of our system.

First NPT

This is a relaxation step, with the number of atoms N, the pressure P and the temperature T all kept constant (NPT step). This is a kind of homogenization of the distribution of atoms inside our box.

NVT

This is also a relaxation step, with atom number, volume and temperature constant.

Second NPT

Now we perform another relaxation NPT to reach lab conditions.

Final NPT

This is the final NPT, which last much longer and gives us the ouput of the simulation.

.conf file

Simulation parameters

For the Constant Pressure Control (so during the variable volume period):

useGroupPressure yes ; # needed for rigidBonds

useFlexibleCell no # no for water box, yes for membrane

useConstantArea no # idem

Initial minimization

This is quite easy to achieve, as NAMD has a specific keyword to run a simulation:

minimize #number of minimization steps

In more details:
Run one step to get into scripting mode

minimize 0

Turn off until later

langevinPiston off

Minimization

reinitvels 5 #reinitialization of all velocities

minimize 100 #no need to run

output min

Heating

We tried different protocol, but this one is the best:

reassignTemp $temp_step ; # starting temp

reassignIncr $temp_step ; # temp increment

reassignHold 300 ; # final temp

reassignFreq 100 ; # num timesteps to temp incr.

For this first step, we wanted a continous growing of temperature, so we used: (here for example from 5 to 30K)

for {set i 5} {$i < 30} {incr i 5} {

set temperature $i

langevinTemp $temperature

run 30}

output heat