Nilesh Dhumal wrote:
Hello
I am trying to run umbrella sampling for my system. I have system with
four ion pairs (4 cation and 4 anion) of ionic liquids and 1024 water
molecules. I am trying to PMF calculation with cation-anion distance as a
reaction coordinate. I choose cation as group1 and anion group2.
I am getting the free energy around ~400 kcal. Can you tell where I am
going wrong?
Given this little detail, no one can do anything but speculate. You haven't
even said how long your simulations are, or how many windows you've used, or how
you generated configurations for the sampling. I could go on. If you want
diagnostics, you've got to provide substantial detail about what you're doing
and how you're doing it.
So let's clarify: you're trying to restrain them all at the same time? That
sounds like a recipe for failure. Presumably these molecules will diffuse
through the water in all directions, but then with the umbrella restraint you're
trying to fix the COM distance of each group.
Why not try to restrain one anion and one cation in a box of water, and
calculate PMF as a function of straight line distance? What is your objective?
If nothing else, a simpler system will tell you if your methods are correct,
if your simulations are long enough, etc.
I have one more question, In my equilibrated strcutrue cations and anions
are far from each other (around 7-8 A). I am more interested in structure
where cation and anion close (around 2-4A)
How can I do the PMF simulation to get this structure.
You have to sample in windows that correspond to this spacing, so you have to
have an input configuration with the desired COM distances. Umbrella sampling
will restrain the configurations at a given distance, as specified in the .mdp
file. It will not allow significant deviation from this position, unless the
spring constant is very weak, in which case you're probably undermining the
purpose of the sampling and need very long simulations.
-Justin
I have pasted pull code used in mdp file.
Nilesh
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = YES ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = EMI
pull_group1 = ETS
pull_init1 = 0.0
pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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