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Re: [lammps-users] Free energy of water
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Re: [lammps-users] Free energy of water


From: Lamm Gro <lammgro@...24...>
Date: Tue, 27 Jun 2017 19:07:22 +0900

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 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 ? 

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.
  


On Mon, Jun 26, 2017 at 10:10 PM, Lamm Gro <lammgro@...24...> wrote:
Dear Axel , 

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

Regards,
Saeed.

On Mon, Jun 26, 2017 at 9:58 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Mon, Jun 26, 2017 at 8:50 AM, Lamm Gro <lammgro@...24...> wrote:
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/softcoul/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 ? 

​there answer is right there: ​

The 
coul/cut/softcoul/long/soft and tip4p/long/soft substyles are designed to be combined with other pair potentials via the pair_style hybrid/overlay 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.​

 

Regards,
Saeed.

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.