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 t
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 of
Thanks a lot.
Valerio
"Justin A. Lemkul" 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 output? So
w
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.
Va
Dear all,
I'm trying to install gromacs 4.5.3, I've succesfully installed fftw
3.3.2 and openmpi 1.4.3
When I try to configure gromacs with
./configure --with-fft=fftw3 --enable-shared --enable-mpi
the shell reply me with this error:
configure: error: cannot compute sizeof (off_t)
See `conf
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:
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 ha scritto:
On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:
Dimitris Dellis wrote:
Hi.
There is an issue w
The dynamic works, but I still have the same problems with minimization...
"Justin A. Lemkul" 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" ha scritto:
vferra...@units.it
Ok and which definition have you used? the previous one with 5 atom
for molecule?
"Justin A. Lemkul" 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 .mdp file you po
Just the last thing... can you copy your mdp file? I think I'm having
some problems also with that... Thanks.
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
I've obtained a stable trajectory for a single CHCL3 molecule. By
setting "continuation = no" (so that constr
Thanks a lot!!!
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
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 nstlist to 5
in md
No, is not working also in this case... probably the problem is with
my mdp files:
for minimization is:
title = Minimization
cpp = /lib/cpp
include = -I../top
constraints = none
integrator = steep
emtol = 5.0
emstep = 0.01
nsteps
Seems that the new definition I've found works, but it is still
unclear to me why...
Valerio
vferra...@units.it ha scritto:
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
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 0.
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 2
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:
http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597
Thanks a lot, but... How can I exctract density information by using g_energy?
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a s
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 authomat
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