Free energy of water

Dear LAMMPS users ,

I want to calculate water free energy by fix adapt/fep command .

The pair-style lj/cut/soft ( http://lammps.sandia.gov/doc/pair_lj_soft.html ) says :

The coul/cut/soft, coul/long/soft and tip4p/long/soft substyles are designed to be combined with other pair potentials via the pair_style hybrid/overlay command. This is because they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if lambda = 1, a singularity may occur.

According to the above mentioned description can you please let me know how I can do this calculation ?
Actually I am not completely familiar with this Fix command I have started reading some papers , I would be grateful if you also can give me some hints about that .

Regards,
Saeed.

Dear LAMMPS users ,

I want to calculate water free energy by fix adapt/fep command .

The pair-style *lj/cut/soft* ( http://lammps.sandia.gov/
doc/pair_lj_soft.html ) says :

​​
The *coul/cut/soft*, *coul/long/soft* and *tip4p/long/soft* substyles are
designed to be combined with other pair potentials via the *pair_style
hybrid/overlay* <http://lammps.sandia.gov/doc/pair_hybrid.html> command.
This is because they have no repulsive core. *Hence, if used by
themselves, there will be no repulsion to keep two oppositely charged
particles from overlapping each other. In this case, if lambda = 1, a
singularity may occur.*

According to the above mentioned description can you please let me know
how I can do this calculation ?

​there answer is right there: ​



The *coul/cut/soft*, *coul/long/soft* and *tip4p/long/soft* substyles are
designed to be combined with other pair potentials via the *pair_style
hybrid/overlay* <http://lammps.sandia.gov/doc/pair_hybrid.html> command​

Actually I am not completely familiar with this Fix command I have started
reading some papers , I would be grateful if you also can give me some
hints about that .

​as this is part of a "user" package, you should contact the authors, that
contributed the package, if they don't respond here on the list within a
reasonable time (say a couple of days).

before doing that, i strongly recommend to study the provided examples.

axel.​

Dear Axel ,

Thanks for your help .
I will be waiting for other’s reply .

Regards,
Saeed.

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

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 12 34 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 12 34 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2

What is the reason of using these atom types separately ? 12 : Methane atoms ----- 34 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 ?

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

Best ,
Saeed.

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 ?!

​what is the charge of an atom that has no interactions?​

...............
fix TPSTAT all npt temp \{TK\} {TK} 100 iso \{PBAR\} {PBAR} 1000

set type 1*2 charge 0.0

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 is the interaction​ for which you want to compute the free energy for
here?

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

​what does the "P" in FEP stand for?

axel.​