You can change integrator back to l-bfgs and the requested atoms will be
non-movable as well. MD in the file is just because I ran EM first and then
MD to check the problem. So, the last keyword is present.
What kind of calculation do you want to perform at all? - It's even better
to run MD for
Mark Abraham wrote:
Syed Tarique Moin wrote:
Hello,
Can anybody help me to get comment from gmx source code via doxygen or
there is some other way for it.
No. You have to download the source and read it.
That is to say, we have been planning to start using doxygen for a
while, and in
I tried Martini force field and found it calculates with a good
result in appearance
for a *specific* calculation prepared at the Martini website.
That is good to know :))
Now, I wish to use another small molecule (such as lipid) for CG
simulation.
Starting from the chemical structure, I
Hello,
on Friday I tried to clone the git repo for the first time, but
unfortunately I was not successful and got following error message:
# git clone git://gromacs.cbr.su.se/gmx-src.git
Initialized empty Git repository in
/Users/dommert/icp/develop/gromacs/gmx-src/.git/
fatal: The
Dear gmx'ers,
Could you explain me the following points in manuals for g_cluster and
g_clustsize programs?
1) Manual for g_cluster:
single linkage: add a structure to a cluster when its distance to any element
of the cluster is less than cutoff...
Other options...
-cutoff real 0.1 RMSD cut-off
Florian Dommert wrote:
Hello,
on Friday I tried to clone the git repo for the first time, but
unfortunately I was not successful and got following error message:
# git clone git://gromacs.cbr.su.se/gmx-src.git
Initialized empty Git repository in
Dmitri Dubov wrote:
Dear gmx'ers,
Could you explain me the following points in manuals for g_cluster and
g_clustsize programs?
1) Manual for g_cluster:
single linkage: add a structure to a cluster when its distance to any
element of the cluster is less than cutoff...
Other options...
* David van der Spoel sp...@xray.bmc.uu.se [2009-07-05 08:36:27 -0400]:
Florian Dommert wrote:
Hello,
on Friday I tried to clone the git repo for the first time, but
unfortunately I was not successful and got following error message:
# git clone git://gromacs.cbr.su.se/gmx-src.git
Florian Dommert wrote:
* David van der Spoel sp...@xray.bmc.uu.se [2009-07-05 08:36:27 -0400]:
Florian Dommert wrote:
Hello,
on Friday I tried to clone the git repo for the first time, but
unfortunately I was not successful and got following error message:
# git clone
Dear gmx users,
By trials, I find a strange thing: After some energy minimizations (EM) in
parallel, steep and cg, the system would explode into parts
unexpectedly(between parts, long distance does not facilitate formation of
covalent bonds as should); However, while running EM not in
Hi,
I am a bit new to gromacs and am familiarizing myself with the various
commands. I want to simulate an unusual molecule, with the formula C7H10.
The downloaded pdb file had the residue mname MON which gromacs does not
recognize. How should i name the residue?
Thanks, David.
Sorry, maybe my questions were too fuzzy.
They concern the definition of cluster in these codes.
1) When we estimate through single linkage whether the structure belongs to the
cluster we should find the smallest distance between any element of the
structure and any element of
In addition to previous letter (Monday is hard-day!)
It looks like I have known the answers to my questions.
Maybe the reason is that the g_cluster code compared to g_clustsize includes
not only single linkage but also other algorithms. So the RMSD feature and
smaller default value of -cutoff
Dear all ,
I am trying to energy minimisation of one protein
molecule but during the grompp mdrun I am facing error again and again like
this-
t = -0.000 ps: Water molecule starting at atom 35705 can not be settled.
Check for bad contacts and/or reduce the timestep.
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