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Re: [lammps-users] lammps-users Digest, Vol 133, Issue 109

From: Agilio Padua <agilio.padua@...24...>
Date: Tue, 27 Jun 2017 14:15:49 +0200


On 27 Jun 2017, at 14:02, wrote:

From: Lamm Gro <lammgro@...24...>
Subject: Re: [lammps-users] Free energy of water
Date: 27 June 2017 at 12:07:22 GMT+2
To: Axel Kohlmeyer <akohlmey@...24...>

Hi . 

I have some questions about fep examples in LAMMPS and I will be grateful if you can answer them : 

1 - in equilibration section of ( lammps/examples/USER/fep/CH4hyd/fep01 ) why we set the charges of methane atoms to zero ?!
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000

set  type  1*2  charge  0.0

The charges are initially set to zero so that the solute does not interact with the solvent, both through the real-space and the k-space parts of the Coulomb potential. (For the real-space part using the lambda would suffice)

run 20000

2 -  fix adapt/fep  and compute fep commands ( lammps/examples/USER/fep/CH4hyd/fep01 )  :  

fix ADAPT all adapt/fep 10000 &
  pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda &
  atom charge 1 v_q1 &
  atom charge 2 v_q2 &
  after yes

 compute FEP all fep ${TK} &
  pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
  atom charge 1 v_dq1 &
  atom charge 2 v_dq2

 What is the reason of using these atom types separately ? 1*2 : Methane atoms  -----  3*4  water atoms 
If we want to set a parameter on methane atoms why we need to mention water molecules ( 3*4 ) in these two commands ? 

What you modify during the free energy calculation are the I-J interaction parameters (cross or unlike interactions).

3 -  Can you please let me know why we need v_dlambda with v_lambda ? 
Actually i can't understand the reason of using this command :      variable dlambda   equal    0.05

lambda is the value of the activation parameter (0: initial system, 1: final)
dlambda is the step in lambda between each stage of activation.

You should study the fundamentals of free energy calculations.

Best regards,
Agilio Padua