On 21/10/2010 10:45 AM, Abhijeet Joshi wrote:
Hi,
I am new to the list. I am trying to simulate lipid
bilayer with atomistic model. I want to calculate surface pressure at
phase boundary. I am thinking of using #surf*surfTen option with
g_energy. But I am afraid, that I won't get
Hi,
I am new to the list. I am trying to simulate lipid bilayer with
atomistic model. I want to calculate surface pressure at phase boundary. I
am thinking of using #surf*surfTen option with g_energy. But I am afraid,
that I won't get a meaningful value because of large fluctuations.
rainy...@yahoo.com wrote:
Justin,
I have a single solute. But I understand what you're saying about the
cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force
field), so therefore, the snapshots corresponding to a minimum periodic
distance of < 1.2 nm would agree with the over
Justin,
I have a single solute. But I understand what you're saying about the
cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field),
so therefore, the snapshots corresponding to a minimum periodic distance of
< 1.2 nm would agree with the overlap witnessed in VMD?
Thanks agai
rainy...@yahoo.com wrote:
Hi Justin,
Thanks for getting back to me. I executed the following command using
g_mindist:
$gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n
index.ndx -od mindist.xvg
..and got the output (see below). It shows that the minimal distance to
per
Hi Justin,
Thanks for getting back to me. I executed the following command using
g_mindist:
$gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx
-od mindist.xvg
..and got the output (see below). It shows that the minimal distance to
periodic image is at the most a few nm
rainy...@yahoo.com wrote:
Hi,
Is there a way to quantitatively determine, from a trajectory file,
whether a molecule is interacting with a copy of itself in the adjacent
box (given that PBC is applied)? Currently, I'm using VMD - I've
already loaded the *xtc file into the*gro structure fil
Hi,
Is there a way to quantitatively determine, from a trajectory file, whether
a molecule is interacting with a copy of itself in the adjacent box (given
that PBC is applied)? Currently, I'm using VMD - I've already loaded the
*xtc file into the*gro structure file and viewed the "periodic images
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