On 13/10/2011 12:35 AM, Nuno Azoia wrote:
I know that from the beginning. That's why I found very strange the
increasing on the system volume. My initial setup have a density of
~400g/L, and for liquid chloroform is ~1400g/L.
Using gromacs-4.5 I get densities of about 200 after 750ps simulation
time, and using 4.0 I get almost 500 after 1ns.
Your chloroform parameters are probably only valid for a condensed
phase, and your initial density is nowhere near that. Please follow the
approach here
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation.
And I was using such low densities because I build the box using
genconf with the options -nbox and -dist, starting with one molecule
of chloroform. If I used small distance values I get LINCS warnings in
the energy minimization step. Using genbox to solvate one empty box
with chloroform, I get very strange behaviors, with a very large
amount of molecule overlap.
Shrug. Without command lines and descriptions of what is in your input,
we are helpless. Please follow the above advice.
But as you said before, I now think that this should be also a
paralelization problem, not to mention the numerical instability
caused by this very low density.
And I think this is a paralelization problem associated with this
numerical instability judging from the system behavior.
In 4.5, using the option -nt in mdrun, I get some small droplets of
liquid chloroform, and in 4.0, using mpi, I get one large droplet of
chloroform. It looks like if 4.5 is treating the system like
independent small systems, while 4.0 is able to divide the system into
small, but interdependent systems.
No, the implementation of parallelization might have an effect here if
you were starting from a reasonable approximation of a condensed phase.
These two observations are just two of the possible things that could
happen to a liquid at extremely low density.
Mark
On Wed, Oct 12, 2011 at 12:26 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 12/10/2011 8:04 PM, Nuno Azoia wrote:
Thank you Mark for your answer!
I agree with you when you say that the high pressure is not itself a
problem. To avoid that problem I change my system from 1000 molecules
to 27000 molecules, and the pressure change from several thousands to
several hundreds bar.
What I found very strange was the increasing volume (and pressure). My
system is very unstable, I know, because the density is very low, and
not the opposite, so I was expecting to see the box getting smaller.
Looking to the trajectory I can see a box almost empty (with empty I
mean empty space, with chloroform molecules aggregating in small
droplets), and that's why I found the system behavior very strange.
Sounds like your initial density might be far too low. grompp reports it, so
do check.
Mark
I will follow your suggestion concerning nsttcouple and nstpcouple and
the other initial conditions.
Nuno Azoia
On Wed, Oct 12, 2011 at 6:24 AM, Mark Abraham<mark.abra...@anu.edu.au>
wrote:
On 12/10/2011 2:22 AM, Nuno Azoia wrote:
Hello!
I found something very strange while making a CHCl3 box using
gromacs-4.5.5.
A look the mailing list, the manual and some release notes for
gromacs-4.5 and I couldn't found the answer for my problem. It's
possible that I'm doing something wrong, but I can not find what, so
I'm describe my problem.
I start a chloroform box from scratch, using genconf, and I get o
chloroform box with 1000 molecules. I get energy minimization without
problems.
Then I've run some equilibration steps in a NVT ensemble and in the
end I get pressure in the order of hundreds of bar.
The high pressure is not itself a problem - small numbers of molecules
and
short simulation times lead to doubtful statistics for pressure.
Then I change to
NPT conditions and both the pressure and the volume keep increasing
with time.
Be sure to visualize your trajectory to confirm its behaviour matches
what
you expect from the trends in P and V.
To discard the possibility of a size problem, I repeat everything with
a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
was the same. Very high pressures (150-200 bar) and very low densities
(< 200 g/L) after 750 ps simulation time. And both volume and
pressure
increasing with time.
I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
getting very different (and better) results. After energy minimization
I run 50000 steps in a nvt ensemble and I got pressure around -30 bar
(Ok for me). After that I start to run the simulations in npt ensemble
and the pressure start to increase slowly, with negative values
because the system have very low densities (~400 g/L), and the volume
is decreasing. So I'm getting the normal reaction from the system.
Where is the problem? There are some different parameters to set in
the mdp file and I didn't realize that, or is this a problem in
gromacs-4.5?
It seems you are generating some numerical instability with your choice
of
initial and simulation conditions, and that gromacs-4.0 was luckier in
avoiding the problem. If this is a parallel simulation, then the way
communication is managed in order to organize T and P coupling changed
going
up to 4.5. For equilibration, I would encourage setting nsttcouple and
nstpcouple to 1. Using a shorter time step can help with numerical
instability. Berendsen T coupling or a larger coupling time constant
might
also help. After gentler NVT, then switch to NPT, let the box size
stabilize, and finally move to larger coupling periods, time steps and
v-rescale T coupling.
Mark
In both cases I used this parameters:
-------------------------------------------------------------------------
integrator = md
dt = 0.002
nsteps = 50000
nstcomm = 1
nstxtcout = 500
xtc-precision = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstenergy = 500
nstlist = 5
ns_type = grid
;Reaction field
rlist = 0.8
coulombtype = Reaction-field
rcoulomb = 1.4
epsilon_r = 1.0
epsilon_rf = 4.8
vdwtype = cut-off
rvdw = 1.4
; temperature coupling
Tcoupl = v-rescale
tc-grps = CHCL3
tau_t = 0.05
ld_seed = -1
ref_t = 300
; Energy monitoring
energygrps = CHCl3
; Isotropic pressure
Pcoupl = no
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300
gen_seed = -1
constraint_algorithm=lincs
lincs_order = 4
lincs-warnangle = 90
constraints = all-bonds
------------------------------------------------------------------------
and of course, for the npt ensemble I just change
_________________________________________
Pcouple = berendsen
gen_vel = no
------------------------------------------------------------------------
Thank you in advance
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