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 cp
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 ex
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 runn
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 c
On 3/31/13 11:41 AM, Elisabeth wrote:
Dear all,
In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need fo
Dear all,
In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need for empty space in Z
Thanks for any comment
Hi,
I obtained the electron density profile for the solvent in protein membrane
simulation,
For this I used the following commands:
]$ g_density -f md.xtc -s md.tpr -d z -dens electron -o sol.xvg -ei
electrons.dat -symm
-n index.ndx
Although in md.gro file is seen any water in m
Hello,
priyanka srivastava <[EMAIL PROTECTED]> wrote: Dear all,
I wish to calculate the density profile of a lipid bilayer i.e the electron
density and this is how I am using the g_density command:
g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm
where electrons.d
Dear all,
I wish to calculate the density profile of a lipid bilayer i.e the electron
density and this is how I am using the g_density command:
g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm
where electrons.dat contains # of electrons information for each and eve
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