On 3/31/13 1:12 PM, Elisabeth wrote:
Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.
Here are the steps:
1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I extended the box in Z to more than twice the initial box size and
issued the following:
grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr
mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v
My questions are:
1) Can I get the proper solvent-air interface to obtain density profile by
extending the Z direction (last line of the gro file obtained from NPT at
each pressure)? Is that what yo mean by " then build a new unit cell and
run under NVT" ?
That's one approach. It's not NVT if you're using pressure coupling, though. I
would also be careful about using the term "air" here - if it's empty space,
it's actually vacuum.
2) Is the semi isotropic option with 0 compressibility in Z is appropriate
to keep the pressure fixed? (as shown below in mdp settings)?
That should work. As long as the dimension along which you need the density
profile is invariant, you should be able to circumvent any issues.
-Justin
3) If the answer to q 2 is negative, whats is appropriate way to shift from
NPt to NVT run. Do I have to use the equilibrated density from NPT runs and
edit the last line of gro from -c flag of NPT.gro to obtain the correct
density? The reason I am asking is that since P fluctuations are huge I am
not sure if the the density of box from last frame of -c NPT.gro output is
the correct density...
Please advise on the above queries..Thanks a lot
Below is the md.mdp contents:
pbc = xyz
integrator = md
dt = 0.001
nsteps = 20000000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100;1
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 1
rvdw-switch = 1 ;0.9
; Cut-offs
rlist = 1.35
rcoulomb = 1.1 ;1.1
rvdw = 1.1
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 425
* *
*Pcoupl = berendsen*
*Pcoupltype = semiisotropic *
*tau_p = 1 0.5 *
*compressibility = 3.5e-5 0*
*ref_p = 50 ** *
gen_vel = no
gen_temp = 500.0
gen_seed = 173529
constraints = none
constraint-algorithm = lincs
On 31 March 2013 12:47, Justin Lemkul <[email protected]> wrote:
On 3/31/13 12:27 PM, Elisabeth wrote:
Thank Justin. I am interested in the density profile at the solvent-air
interface. I wanted to see how density changes with position at different
pressures...I have the equilibrated boxes at several pressures obtained
from NPT but I am not sure whether running g_density on the current
simulations cells provides the profile I am after. Do you have any clue
whether or not the cell has to be extended in one direction to obtain the
density profile?
If you're trying to produce an air-water interface, then indeed you will
need some model for air within the unit cell, but there are several
practical problems with that. The first is that g_density does not deal
well with changing box vectors, and the density profiles it produces under
an NPT ensemble are incorrect (outstanding bug that needs to be fixed,
IIRC). The second is that if you run a simulation under NPT with void
space, the unit cell will just compress down until there is no empty space.
Probably the best solution would be to equilibrate under NPT at the
desired conditions, then build a new unit cell and run under NVT. Using
NVT will circumvent both problems, and if the proper pressure, density, etc
have already been achieved, then you've got what you're after.
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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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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