AMBER Archive (2008)

Subject: Re: AMBER: Discontinuous Constant pH Restarts

From: David A. Case (
Date: Fri May 02 2008 - 14:44:31 CDT

On Thu, May 01, 2008, Neil Bruce wrote:
> I am trying to perform constant pH simulations, but am having problems
> when restarting simulations. Below is the energy data of the last step
> of one trajectory and the first step of a restarted trajectory. As you
> can see there is a large jump in the potential energy of the system.
> NSTEP = 40000 TIME(PS) = 180.000 TEMP(K) = 299.71 PRESS
> EELEC = -3128.8680 EGB = -2220.8243 RESTRAINT =
> ------------------------------------------------------------------------------
> NSTEP = 1 TIME(PS) = 180.002 TEMP(K) = 293.59 PRESS
> EELEC = -3472.0209 EGB = -1146.9263 RESTRAINT =

It's weird that the EGB energy is like a factor of 2 there any
possibility of a different intdiel or extdiel factor in the second run?

You could explore this more by running two short simulations (say 50 steps
each) where you set ntpr=1, and restart the second from the end of the first.
Then compare that to a single 100 step run from the initial starting point.
Using a smaller time step might also help identify restart problems.

I'm cc-ing this to John Mongan, but I don't recognize the symptoms myself.

> Examining the cpout files shows that the protonation states are being
> carried over into the restarted simulation as the initial states in
> the restarted simulation match the end of the preceeding simulation. I
> have tried using both formatted and unformatted restart files and
> increasing cut and rgbmax, with the same result. Below is the mdin
> file and the command used to run sander for the restarted simulation
> (the mdin file for the initial simulation differs only in irest, ntx
> and tempi):
> &cntrl
> imin=0, irest=1, ntx=5,
> icnstph=1, solvph=7.1, ntcnstph=5,
> nstlim=40000, ntpr=1, ntwx=200,
> cut=30.0, scee=1.2, igb=2, saltcon=0.1,
> ntb=0, dt=0.002, nrespa=1,
> ntt=1, temp0=300., tautp=2.0,
> ntc=2, ntf=2, tol=0.000001,
> /
> sander.MPI -O -i -p pep.prmtop -c constph.rst1 -cpin
> constph.cprst1 -o constph.out2 -x constph.mdcrd2 -r constph.rst2
> -cpout constph.cpout2 -cprestrt constph.cprst2


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