On 9/04/2010 1:25 PM, jampani srinivas wrote:
Dear Justin,
I am sorry for the poor description of the problem, OK let me explain
you clearly here.
I have taken a decapeptide and solvated it with box size 6.0 nm, I want
to create a frozen wall (confined sphere) around protein after a certain
radius (in this case it is 2.5 nm). To achieve this i made two
temperature coupling groups, first (Tmp1) one has protein and waters
within 2.5nm from the center of the box and rest is second temperature
coupling group (Tmp2). Initially when i run the simulation it was
creating nrdf = 0 for both groups, Berk has helped me with a file
readir.c file, i compiled my gromacs again that problem was solved. I
have submitted simulations again and found that the energy was blowing
up. I think you know the story after this. Earlier I want protein to
interact with inner wall of the frozen group and check what happens,
because of this I have never looked at the energygrps_excl option. I
have done with both 2 and 4 fs time steps and I took 4fs option to speed
up the simulation, and I have to still look at the paper you suggested me.
Thanks for your suggestions, I have implemented your suggestion one
after the other, finally when i use the energygrps_excl option it worked
out. Now there is no sudden drift in the energy, and also i checked the
velocities of non-frozen group is mostly zero (except for first frame)
When I use the energygrps_excel option in the following way i am getting
the below mentioned note i have to still understand what is this
message. On the other hand if i use only "energygrp_excl = Tmp2 Tmp2
Tmp2 Tmp1" line in mdp file i am getting fatal error. Is it necessary
to to define the energy groups first and later exclude the energy option?
Yes, energy group exclusions require matching energy group definitions.
The relevant part of manual 7.3 probably says this.
+++++++++++++++++++++++++++++
energygrps = Tmp1 Tmp2
energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1
++++++++++++++++++++++++++++++++
NOTE
"Can not exclude the lattice Coulomb energy between energy groups"
You seem to be trying to simulate a droplet inside a rigid shell of
water. If so, why do you want the system to be periodic? You don't want
periodicity artefacts *and* frozen-water-shell artefacts. There are
other electrostatics models better suited than PME to such situations.
You should look in the literature for successful published
methodologies, rather than risk inventing a square wheel yourself before
you've got enough experience to be confident with what you're doing.
Here, the reciprocal-space part of the PME calculation must contain
contributions from your excluded energy-groups, so you've got some
Frankenstein possible worst-of-all-worlds combination. If I got such a
paper to review, I'd need to see some serious groundwork justifying such
a choice.
I used -maxwarn option here and generated the tpr file. I hope this does
not harm the simulation.
That's a risky strategy. The programmer didn't put in such a message
just to see whether he could do it...
Mark
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