Dear Gromacs experts and users,
I am here to seek help. I want to use constraint pull method to pull a
filament. My plan is to keep the center of mass of one group fixed
through a stiff restraint, say 3×10e5, and pull the other group. I tried to
generate the restraint .itp file and modify the
Dear All,
The command trjcat can be used for connection of trr files and xtc files in the
similar manner, and suppose the first MD is from 0 to 1 ns, the second MD is
from 1 ns to 4 ns, the third MD is from 4 ns to 4.5 ns, by trjcat we can get
the whole trr file from 0 nx to 4.5 ns, and if
Dear Users
I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled
structure holding ATP, water and TPO as hetero atoms. but I am faced with the
following error. I checked all LUE residues (although I have got no residue
with 28215089 number) and I found no missing atom N. I
Right.
Note that trjcat can also convert the file format.
Cheers,
Tsjerk
On Jul 5, 2015 9:32 AM, Brett brettliu...@163.com wrote:
Dear All,
The command trjcat can be used for connection of trr files and xtc files
in the similar manner, and suppose the first MD is from 0 to 1 ns, the
On 7/5/15 12:56 AM, Christopher Neale wrote:
Dear Justin:
Thank you for your help. I am glad to see that I was not way out to lunch in my
interpretation of multiplicity and proper dihedral angles.
First, the out-of-plane motions are not minor. Even just in EM, the dihedral
angles along the
g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean?
If this is a probability than of what?
@title Cluster size distribution
@xaxis label Cluster size
@yaxis label ()
@TYPE xy
0 0.000
128.385
2 7.135
3 1.552
4
Dear Justin:
here is a topology followed by initial coordinates (in which the rings of both
Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and
the SC ring of Phe #1 will distort. However, replace 0 15.1669998 2 by 180
15.1669998 2 and everything is groovy.
I do now know what authors meant. However, the COM-COM pulling implies
that one group is restrained and another group moves relative to it.
So, the COM of the reference group is already fixed in the pull code.
On Sun, Jul 5, 2015 at 4:02 AM, Ming Tang qut20181...@gmail.com wrote:
Dear Gromacs
On 7/5/15 9:10 AM, Christopher Neale wrote:
Dear Justin:
here is a topology followed by initial coordinates (in which the rings of both Phe are planar,
straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort.
However, replace 0 15.1669998 2 by 180
On 05/07/15 14:09, V.V.Chaban wrote:
g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean?
If this is a probability than of what?
Probability of cluster size, what else?
@title Cluster size distribution
@xaxis label Cluster size
@yaxis label ()
@TYPE
I see, thank you Justin. I guess that even though I did read the equation,
which is:
K(1 + cos(n*phi - phi_s)
I was actually thinking:
K(1 + cos(n* [ phi - phi_s ] )
so everything is as it should be.
Thanks for all your help,
Chris.
From:
The sum of these probabilities is never the same. It is confusing.
If no clusters exist (all particles are lone) then the sum of
probabilities equals the sum of all particles. If clusters exist, the
sum is different and it is unclear how it is derived.
If the output property is still a
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