Re: Rep: [CP2K:3667] reaction coordinate constrained MD

Sandeep Kumar Reddy kuma... at gmail.com
Sun Dec 11 03:39:08 CET 2011


Dear Ross,
                   To use thermodynamic integration, you use Lagrange
multipliers in put your input file.

input file should look like


   &COLLECTIVE
      COLVAR 1
      INTERMOLECULAR  T
      TARGET [angstrom] 1.0
      TARGET_GROWTH [angstrom*fs^-1] 0.1
      TARGET_LIMIT [angstrom] 1.2
    &END
    &LAGRANGE_MULTIPLIERS ON
      COMMON_ITERATION_LEVELS  3
    &END
  &END



The average of lagrange multiplier gives the mean force acting on reaction
coordinate.   Read "Computation of the pK of liquid water using coordination
constraints" by Sprik  (Chemical Physics 258 (2000) 139,150)  for details
about this method.  This will also tell you how to remove the error
introduced during the thermodynamic integration.

Carry out the simulation at many no. of  distances.  Integration of these
forces give you the free energy.

Regards,
Sandeep


On Sun, Dec 11, 2011 at 7:02 AM, shoutian sun
<sunshou... at yahoo.com.cn>wrote:

> Dear Sandeep,
> Thanks for your reply. Actually, I want to use the
> Thermodynamic integration, and I have no experience
> on this method. Could give me some advice?
>
> Look forward to your reply.
> Best regards,
> Ross,sun
>
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