Sorry but the help does not help me... In anycase, the help of
g_rmsdist say: g_rmsdist computes the root mean square deviation of
atom distances, which
has the advantage that no fit is needed like in standard RMS deviation as
computed by g_rms...; so no fit is needed, for me it means that
Dear all,
I need to calculate the RMSD of a protein during time. So that I've
calculated the trajectory; for the calculation which tool should I
use? g_rms or g_rmsdist ? Which is the difference between these two
tools? If I'm right the main difference is that with g_rms the
structure at
Dear all,
I want to calculate the density of my system and visualize it during
the simulation time. I've tried with g_density and with g_energy but
in all the cases the density calculated is the average density all
along the simulation and not the density of all the system in each
step
Dear all,
I want to calculate the C-alfa fluctuation of a protein during a
trajectory with g_rmsf but I have just one question about the otput:
which is the difference using -o output and -od output? So what is the
difference between fluctuation and deviation?
Thanks a lot in advance.
Thanks a lot.
Valerio
Justin A. Lemkul jalem...@vt.edu ha scritto:
vferra...@units.it wrote:
Dear all,
I want to calculate the C-alfa fluctuation of a protein during a
trajectory with g_rmsf but I have just one question about the
otput: which is the difference using -o output and -od
Sorry, but changing the definition and using the other suggested by
Dimitris doesn't change the results, I still have the same problem in
minimisation...
Valerio
Dimitris Dellis nte...@gmail.com ha scritto:
On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:
Dimitris Dellis wrote:
Hi.
Dear Anna,
I think it's better to keep one single force field... I don't know
which ff is better for your simulation, but for example you can
manually correct the definition that PRODRG gives you and adjusting it
for GROMOS 53a6 paramenters.
Valerio
anna.marabo...@isa.cnr.it ha scritto:
Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer works
good, but I have some problems with the CHCL3 definition in GROMOS
53a6 ff.
I've taken the CHCL3 definition from the automated topology builder website:
I've just tried with a single CHCL3 molecule, here's the output:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition
The molecule is rigid because it's all constrained and the coordinates
of the single molecule seem to be ok:
CLF
5
1CLFCCl1 3.041 1.571 0.924
1CLFHCl2 3.001 1.637 0.845
1CLFCL13 3.071 1.661 1.073
1CLFCL24 3.186 1.493
Thanks a lot!!!
Valerio
Justin A. Lemkul jalem...@vt.edu ha scritto:
Justin A. Lemkul wrote:
snip
I've obtained a stable trajectory for a single CHCL3 molecule. By
setting continuation = no (so that constraints are not solved
before step 0) in the em.mdp file, and then reducing
Ok and which definition have you used? the previous one with 5 atom
for molecule?
Justin A. Lemkul jalem...@vt.edu ha scritto:
vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm
having some problems also with that... Thanks.
For EM, I used the
The dynamic works, but I still have the same problems with minimization...
Justin A. Lemkul jalem...@vt.edu ha scritto:
vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom
for molecule?
Yes.
-Justin
Justin A. Lemkul jalem...@vt.edu ha
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the density and it is waiting for a replay that
I can't
14 matches
Mail list logo
