MD simulation in the canonical ensemble

We will be trying the Nosé-Hoover thermostat (see the Gromacs 4.5 manual on pp28, Chapter 3.4.8).

Instead of setting \(Q\), we’ll specify the period of the oscillations \(\tau_T\)

\[\tau_T = 2\pi\sqrt{\frac{Q}{T_0}}\]

for a desired temperature \(T_0\) (this is the definition of \(Q\) used in Gromacs).

We want to see how the oscillaton time influences the thermostat behavior. Start with \(\tau_T = 1 \mathrm{ps}\) and then try 0.01 ps and 100 ps.

Thermostat selection

Create an appropriate run parameter (MDP file) based on the NVE input file NVE_opls.mdp (which does not have temperature coupling).

In particular, pay attention to

• run length (nsteps)
• temperature coupling algorithm (see the Temperature coupling section in the MDP manual page) — you need to set coupling time, reference temperature \(T_0\), and couple the thermostat to the whole system (group “SYSTEM”)
• temperature: run at 310 K

Use the manual on the MDP options to write your MDP file.

Make a separate directory for each run that you plan to do. Copy the MDP file to each directory and adjust it there. You can take the water.top and em.gro that you generated previously.

Generate TPR file with grompp:

grompp -f MDP -p ../top/water.top -c ../emin/em.gro -o md.tpr

Run the simulation:

mdrun -v -s md.tpr -deffnm md

If it takes too long on your workstation, run it on saguaro on 4 or perhaps 8 cores.

Running on Saguaro

http://a2c2.asu.edu/rails/topics/first-things-first

• login to saguaro (http://a2c2.asu.edu/rails/topics/first-things-first/how_tos/connect-to-saguaro):

  ssh -l USERNAME saguaro.fulton.asu.edu

• create a work directory for this session (note: you’re not sharing space with anyone else), eg

  mkdir P14

• Transfer TPR file and queuing system script saguaro.pbs:

  scp md.tpr saguaro_gromacs.pbs USERNAME@saguaro.fulton.asu.edu:P14/

• increase wall time from 01:00 minutes to 5:00 minutes; Gromacs will stop cleanly after (-maxh) 0.0833 * 1h = 5 mins.

  Note: adjust -maxh depending on your walltime!!

• the -A switch is important so that the time is billed to the course project!

• Submit job to the PBS queing system:

  qsub saguaro.pbs

• Check status:

  qstat
  

• When done, copy stuff back using scp or rsync:

  rsync -avP USERNAME@saguaro.fulton.asu.edu:P14/ .

  will copy all contents of director P14 on saguaro to the current directory (see man rsync for details).