AMBER Archive (2008)

Subject: AMBER: Discontinuous Constant pH Restarts

From: Neil Bruce (Neil.Bruce_at_postgrad.manchester.ac.uk)
Date: Thu May 01 2008 - 08:41:21 CDT

Dear Amber Users

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
= 0.0
  Etot = -1737.1344 EKtot = 608.9854 EPtot =
-2346.1197
  BOND = 158.5661 ANGLE = 435.4544 DIHED =
  412.2094
  1-4 NB = 160.2405 1-4 EEL = 2101.5192 VDWAALS =
-264.4170
  EELEC = -3128.8680 EGB = -2220.8243 RESTRAINT =
    0.0000
  DV/DL = 115.5001
   
------------------------------------------------------------------------------

  NSTEP = 1 TIME(PS) = 180.002 TEMP(K) = 293.59 PRESS
= 0.0
  Etot = -814.3382 EKtot = 596.5487 EPtot =
-1410.8869
  BOND = 156.3082 ANGLE = 450.9187 DIHED =
  412.9435
  1-4 NB = 159.3379 1-4 EEL = 2292.3755 VDWAALS =
-263.8235
  EELEC = -3472.0209 EGB = -1146.9263 RESTRAINT =
    0.0000
   
------------------------------------------------------------------------------

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 constph.in -p pep.prmtop -c constph.rst1 -cpin
constph.cprst1 -o constph.out2 -x constph.mdcrd2 -r constph.rst2
-cpout constph.cpout2 -cprestrt constph.cprst2

Can anyone see any errors that I am committing, or has anyone run into
similar problems in the past?

Any help will be appreciated.

Neil
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu