Wikipedia seems to have these... http://en.wikipedia.org/wiki/Water_model.
The authors of a technique using a version of SPC/E will have to have
referred to the parameterization of that model, whether flexible or not.
Mark
On Tue, Feb 18, 2014 at 2:38 PM, leila salimi leilasal...@gmail.com
Hello GMX users,
I hope you could help me solving this un-understandable (at least for me)
error.
I am trying to run g_cluster on one of my collected trajectories using the
following command
g_cluster -f allnj_1.xtc -n index.ndx -o -g -dist -ev -sz -tr -ntr -clid
-cl -cutoff 0.5 -skip 10 -s
Dear User,
Can you please write me how to build a system of a protein (nonsymetric
obviously) and place it in the on the box edge so that one half is within
the unit cell and another one is copied across pbc on the other side? I
assume I will get the error doing manually...
please, advise.
Building all-against-all matrices takes a lot of memory, and if it runs
out, then crazy things happen. I suggest you start with versions of your
trajectories sampled very sparsely so there are few tens of samples, and
get a sane result from g_cluster from that. Then scale up / find a lot of
memory
Thanks a lot!
Can you please give me a hint how to apply umbrella sampling to the system
of 4 nanotubes with pbc across xyz so that they infinite in length in z
coordinate and 2 of them placed with its half to the unit cell copied
across y coordinate... I want to see PMF minima (equilibrium
On 2/18/14, 1:37 PM, Steven Neumann wrote:
Thanks a lot!
Can you please give me a hint how to apply umbrella sampling to the system of 4
nanotubes with pbc across xyz so that they infinite in length in z coordinate
and 2 of them placed with its half to the unit cell copied across y
Dear GMX users ,
I uploaded a python script to the user contributions section of the GROMACS
website (http://www.gromacs.org/Downloads/User_contributions/Other_software),
it's called readHBmap.py.
The idea behind the script is to allow the user to read the hydrogen bond map
matrix file
Or maybe just 2 of them in the box: so that the one in the cell and another
one has its quarter in the unit cell edge and the free energy between them?
Then this PMF take into account all of the others being copied around.
Would US mdp option wont complain?
Steven
On Tue, Feb 18, 2014 at 7:49
On Fri, 7 Feb 2014, Justin Lemkul wrote:
On 2/7/14, 6:08 PM, Antonio Baptista wrote:
Dear all,
This is a follow-up to an old thread on g_principal, which continues (as of
version 4.6.5) to suffer from what I would call a bug or, at least, a very
bad
and misleading choice of output file
It shows as active to me...
Mark
On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista bapti...@itqb.unl.ptwrote:
On Fri, 7 Feb 2014, Justin Lemkul wrote:
On 2/7/14, 6:08 PM, Antonio Baptista wrote:
Dear all,
This is a follow-up to an old thread on g_principal, which continues (as
of
Szilárd already activated it a couple of hours ago (just noticed he
replied to me only). The issue is already submitted also. Thanks anyway.
Best,
Antonio
On Wed, 19 Feb 2014, Mark Abraham wrote:
It shows as active to me...
Mark
On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista
I am trying to run a simulation of single Na ion in implicit solvent(water),
with OPLSAA FF in gromacs 4.5.7. After running the simulation and viewing
the .log file I find that the initial temperature is set to 0 K even though
I have mentioned a ref_t as 300 K. Why does this happen? Any help is
Can any body explain how to calculate RMSD of only alpha helix and beta sheet
of a protein in
Gromacs
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