Re: [lammps-users] lammps-users Digest, Vol 134, Issue 83

[Agilio Padua <agilio.padua@...24...>]

From: Lamm Gro <lammgro@...24...>

Subject: [lammps-users] Free energy

Date: 26 July 2017 at 07:16:46 GMT+1

To: lammps-users <lammps-users@lists.sourceforge.net>

Dear Lammps users ,

I try to calculate the free energy of water with FEP method .

( free energy of one water molecule inside of a box of it ) .

Unfortunately I just get 0.0 amount for free energy ! 

Can you please let me know what might be problem ?

Does your installation reproduce the tests/examples?

If so, maybe you should proceed in small modifications from there until you fully understand the commands.

I am not going to check your input file line by line. However, some things look strange.

- As I see types 3 4 is the “solute” and 1 2 is the “solvent”. So why do you use soft potentials for solvent-solvent interactions?

- I J pairs should by given as I <= J

- you should adapt the lambdas on Hw-* interactions too because it affects the real space part of Coulomb. 

- the delta in activation parameter lambda seems very small and the number of timesteps at each stage very large. It should be possible to have a good value of free energy with less effort (my guess).

Maybe there are more issues.

As I wrote to you a few times before, this does not seem to be the good method to learn.

Agilio

This is a part of my input file : 

=================================================

pair_style  hybrid lj/cut/tip4p/long/soft 2 1 1 1 0.1546 2.0 0.5 10.0 12.0 &

          lj/cut/tip4p/long 4 3 1 1 0.1546 12.0

kspace_style pppm/tip4p 1.0e-4

pair_modify tail no

pair_coeff    1    1  lj/cut/tip4p/long/soft 0.0000  1.0000 1.0  # HW-Hw

pair_coeff    1    2  lj/cut/tip4p/long/soft 0.0000  1.0000 1.0  # HW-OW 

pair_coeff    2    2  lj/cut/tip4p/long/soft 0.1852  3.1589 1.0  # Ow Ow

pair_coeff    1    3  lj/cut/tip4p/long/soft 0.0000  1.0000 0.0  # HW-HW 

pair_coeff    1    4  lj/cut/tip4p/long/soft 0.0000  1.0000 0.0  # HW-OW 

pair_coeff    2    3  lj/cut/tip4p/long/soft 0.0000  1.0000 0.0  # OW-HW 

pair_coeff    2    4  lj/cut/tip4p/long/soft 0.1852  3.1589 0.0  # OW-OW 

pair_coeff    3    3  lj/cut/tip4p/long      0.0000  1.0000   # HW-HW 

pair_coeff    3    4  lj/cut/tip4p/long      0.0000  1.0000   # HW-OW 

pair_coeff    4    4  lj/cut/tip4p/long      0.1852  3.1589   # OW-OW 

bond_coeff    1       450    0.9572

angle_coeff   1       55     104.52

set type 1 charge   0.5564

set type 2 charge  -1.1128

set type 3 charge   0.5564

set type 4 charge  -1.1128

fix fshake all shake 0.0001 20 0 b 1 a 1

velocity   all create 300 432567 dist uniform

neighbor        2.0 bin

neigh_modify    delay 0 every 1 check yes

set type 3*4 charge 0.0

timestep 1.0

fix P1 all npt temp 300.0 300.0 100 iso 1.0 1.0 1000

run 20000000

 

reset_timestep 0

variable lambda equal ramp(0.0,1.0)

variable q3  equal 0.5564*v_lambda

variable q4  equal -1.1128*v_lambda

fix adapt all adapt/fep 5000000 &

  pair lj/cut/tip4p/long/soft lambda 3*4 1*2 v_lambda &

  atom charge 3 v_q3 &

  atom charge 4 v_q4 &

  after yes

fix pnt all print 5000000 "adapt  lambda = ${lambda} q3 = ${q3}  q4 = ${q4}"

variable dlambda equal 0.01

variable dq3  equal 0.5564*v_dlambda

variable dq4  equal -1.1128*v_dlambda

compute FEP all fep 300.0 &

  pair lj/cut/tip4p/long/soft lambda 4 2 v_dlambda &

  atom charge 3 v_dq3 &

  atom charge 4 v_dq4

fix FEP all ave/time 1000 5000 5000000 c_FEP[1] c_FEP[2] file FEP01.txt

run 100000000

=======================================================

Best Regards,

Saeed.

<data.water><in.fep>

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