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


From: Agilio Padua <agilio.padua@...24...>
Date: Wed, 26 Jul 2017 09:29:12 +0100


From: Lamm Gro <lammgro@...24...>
Subject: [lammps-users] Free energy
Date: 26 July 2017 at 07:16:46 GMT+1


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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