Dear all:
Does anyone know the optimal force field in GROMACS for treating divalent
ions in explicit solvent? Would appreciate any recommendations.
Thanks,
Lili
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Hello,
I am fairly new to using Gromacs and am writing to seek clarification on the
g_rdf module.
In the manual, it states that g_rdf calculates radial distribution
functions in different ways. The normal method is around a (set of)
particle(s), the other method is around the center of mass of a
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
again,
Lili
On 20 October 2010 13:58, Justin A. Lemkul jalem...@vt.edu wrote:
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
Dear GMX users,
I have a quick question regarding which Gromacs force field in pdb2gmx is
best suited for creating a topology (itp) file for the enzyme, lactate
oxidase. So far the force fields in Gromacs 4.0.4 are:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane
/msg14945.html
-Lili
On 25 March 2010 18:13, Justin A. Lemkul jalem...@vt.edu wrote:
rainy...@yahoo.com wrote:
Dear GMX users,
I have a quick question regarding which Gromacs force field in pdb2gmx is
best suited for creating a topology (itp) file for the enzyme, lactate
oxidase. So far
it figured
out :). Thanks for your concern though.
On 25 March 2010 19:22, Justin A. Lemkul jalem...@vt.edu wrote:
rainy...@yahoo.com wrote:
Hi Justin,
I did not mention that I am indeed trying run Gromacs implementing the
MARTINI force field. I realize this is not as automatic as selecting
~
2009/11/13 Justin A. Lemkul jalem...@vt.edu
rainy...@yahoo.com wrote:
Hi all,
I've encountered a problem while trying to run Gromacs on my
coarse-grained molecule. I've already performed the initial energy
...@anu.edu.au
rainy...@yahoo.com wrote:
Hi all,
I've encountered a problem while trying to run Gromacs on my
coarse-grained molecule. I've already performed the initial energy
minimization. I tried to run the inital MD simulation, but the job was cut
short due to a segmentation fault, as mentioned
? Try to
find if everything went ok until the segmentation fault by saving log and
trajectories.
amit
On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
rainy...@yahoo.com wrote:
Hi,
The relevant lines of my script are the following:
line 27: # Run MD and write
Hi all,
I've encountered a problem while trying to run Gromacs on my coarse-grained
molecule. I've already performed the initial energy minimization. I tried
to run the inital MD simulation, but the job was cut short due to a
segmentation fault, as mentioned in the output file:
^Mstep 0^Mstep
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