Hi Anu,
I just have a few things to add:
- after the first iteration, check the density profile after spline
smoothing in .smooth.dens (compare to the raw density file in
.dist.new). If there are oscillations, you have to tune the spline
parameters.
- I am not sure postupd scale applies, but you can as well simply
reduce the prefactor to see if it is to high ( this may very well be
if your CG model has a different compressibility)
- Increase the total simulation time per iteration step and trash some
of the trajectory in the beggining using gromacs.equi_time in the
settings file
Good luck!
-Sebastian
Zitat von Christoph Junghans <[email protected]>:
Hi,
2012/10/31 Anu Nagarajan <[email protected]>:
Hi,
I am trying to run the thermodynamic force using csg_inverse. I have the
settings.xml file with appropriate options for my system. But, when I try to
run TF, I get about 2-3 iterations after which the temperature gets really
high and the system becomes unstable. I have the latest version (1.2.3) of
votca. I computed the prefactor based on the compressibility of the
atomistic region. According to the tutorial and the paper, I have set the
TF range to be d(skin)+d(at)+d(hy)+d(skin) where d(skin) is right now half
the cutoff distance. The entire molecule is one charge group and I have 12
atoms plus virtual site. Do I have to change any values in the settings.xml
file? Is there anything I might be missing?
The parameters will depend on the system you study.
Here are some things you could try:
- increase adress_ex_forcecap in the mdp file
- increase the spline grid (spline_start, spline_end in
cg.non-bonded.inverse.tf) in setting.xml
- add a cg_prefactor in cg.non-bonded.inverse.tf, which is based on
the compressibility of the cg model
- scale the update (add postupd task scale) by something < 1
Sebastian, please add stuff if I have missed something.
Christoph
I appreciate any help in this matter!
Thanks!
Anu
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