On 1/5/16 2:25 PM, Chang Woon Jang wrote:
Dear Justin,
I am curious about resizing the box. My system contains 15000 atoms
representing liquid polymer with very low density (maybe gas phase due to
very low density). Does this very low density affect the simulation not to
converge the box? Or, do the initial conditions (Pcoupl=berendsen,
Pcoupltype=isotropic, tau_p=5.0, compressibility=4.5e-5, ref_p=1.0) in
gromapp.mdp affect? Do I need to test these conditions? I am just starting
to use GROMACS for obtaining atomistic trajectory compatible with VOTCA
coarse-graining package.
Those settings should be fine. Extract the box vectors from the .edr file and
see how much they fluctuate; the final snapshot is not necessarily
representative. But the fact that the box size is exactly the same from start
to finish suggests there is something incorrect (or at least, really weird)
going on. Provide the full text of your .mdp please, not just the section you
think is relevant.
-Justin
The same configuration in LAMMPS works fine.
Thank you.
Best regards,
Changwoon Jang
On Tue, Jan 5, 2016 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/5/16 1:42 PM, Chang Woon Jang wrote:
Dear Abhishek Khetan,
Thank you for your answer. It means that Gromacs does not automatically
adjust the box size even though NPT ensemble is employed. Am I right?
This is incorrect. The box size will change under the influence of
pressure. Its shape should be conserved. But if you're seeing the exact
same box vectors before and after the simulation, something went wrong with
your input.
Different from Gromacs, Lammps automatically adjust box size when NPT
ensemble is applied during the simulation. Therefore, the density is able
to be fitted with initial conditions (pressure, temperature, simulation
time).
GROMACS does this, too.
When I used the "gmx editconf" to resize the box to correct a density, vmd
shows a very ugly configurations. I think that topology file will check
the
bond informations no matter how the gro file, containing only atom
coordinates and box size, looks like.
Indeed, editconf is not useful here. It scales coordinate positions to
achieve the desired density. This is not what you want.
-Justin
If I am wrong, please correct me.
Thank you.
Best regards,
Changwoon Jang
On Tue, Jan 5, 2016 at 1:16 PM, abhishek khetan <askhe...@gmail.com>
wrote:
To rescale the box.gro to a desired size using the actual density 543.21
kg/l of the solvent and get a new scaled.gro file, I use this command:
$ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile
On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang <changwoonj...@gmail.com
wrote:
Dear Gromacs Users,
I have a low density polymer system initially. I would like to fit the
correct liquid density using NPT simulation.
I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is
still
the same as the input size of conf.gro.
Initial in conf.gro (10.0 10.0 9.8)
output in confout.gro (10.0 10.0 9.8)
My initial conditions are
tau_p=5.0
compressibility=4.5e-5
ref_p=1.0
Do I need to increase compressibility?
Thank you.
Best regards,
Changwoon Jang,
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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