i used the pdb2gmx command but i get a message command not found. can you
help me
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Set the installed path and library path of Gromacs in .bashrc file and
source it
On Tue, Apr 1, 2014 at 1:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.comwrote:
i used the pdb2gmx command but i get a message command not found. can you
help me
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I don't know, I just follow the instruction. What information should I need
to give?
On Tue, Apr 1, 2014 at 1:55 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 01.04.2014 08:29, Ly Minh Nhat wrote:
Well, I have solve the first error by installing g++. The fftw error still
On 01.04.2014 10:36, Ly Minh Nhat wrote:
I don't know, I just follow the instruction. What information should I
need to give?
It's on the fftw3 install page
(http://www.fftw.org/doc/Installation-on-Unix.html)
in the first item:
• --enable-float: Produces a single-precision version of FFTW
Please please read the basics (i.e. how to use) about Gromacs before
posting questions.
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dear users
i am trying to make a .xtc file from an existing .trr and exclude some frams of
.trr file. should i be using trajconv to cut the trajectory around the
nonwanted frames and fuse the wanteds by trajcat? is there any other way to do
it in a single command?
regards,
saman
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Thank you Justin for your reply.
Yes I am getting unfolded configurations at higher temperature (loss of
native contacts and increase in Rg). I have used NPT ensemble.
Is it that we cannot compare number of contacts at two different
temperatures using NPT ensemble? Or is there any normalization
On 3/31/14, 10:29 PM, Pappu Kumar wrote:
Decoupling seems only feasible for small ligands. I tried to decople a protein
but the grompp does not converge. Could you tell me the maximum size of the
molecule that is feasible for decoupling? I already calculated the free energy
of solvation by
Many thanks to both of you! :)
I am not that familiar with C-Code and gromacs. Maybe you could take a look
at it, that this would be correct for me? Does this code also work for none
cubic boxes?
// Here begins the actual analysis
static int analyze_frame(t_topology *top, t_trxframe *fr, t_pbc
I would try this one:
trjconv -f traj.trr -o traconv.xtc -b 0 -e 25
This line exports just the first frames from your trajectory traj.trr. Now
you have the change the values behind -b and -e, depending on your settings.
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View this message in context:
Not so far. You are comparing the results of two different chaotic
processes - see
http://www.gromacs.org/Documentation/Terminology/Reproducibility
Mark
On Tue, Apr 1, 2014 at 1:05 AM, Rafael I. Silverman y de la Vega
rsilv...@ucsc.edu wrote:
Hi all,
I am running a nvt position restrained
Thank you Justin for your valuable reply. But you know, my box size is
17.744*17.744*17.744 nm^3. I have used editconf -bt cubic -f
20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6 to generate the box. And
the full description of the box size I have used is
Read 15484 atoms
No velocities found
On 4/1/14, 12:56 PM, Kalyanashis wrote:
Thank you Justin for your valuable reply. But you know, my box size is
17.744*17.744*17.744 nm^3. I have used editconf -bt cubic -f
20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6 to generate the box. And
the full description of the box size I have used
On 4/1/14, 2:18 PM, Kalyanashis wrote:
Thank you so much Justin. Now I am trying with a rectangular box. I don not
whether it will work or not.
There shouldn't be any guesswork involved. You know what the initial COM
separation is (or you can easily calculate it or wait for grompp to
Thank you so much Justin. Now I am trying with a rectangular box. I don not
whether it will work or not.
On Tue, Apr 1, 2014 at 10:51 PM, Justin Lemkul [via GROMACS]
ml-node+s5086n5015553...@n6.nabble.com wrote:
On 4/1/14, 12:56 PM, Kalyanashis wrote:
Thank you Justin for your valuable
a) Did you mean build as make a build folder? If so, then yes. My process
is mkdir build, cd bulid, cmake .., make, make install.
b) I load enviroment variable during cmake: cmake ..
-DCMAKE_PREFIX_PATH=/usr/local
There is no output for source /usr/local/gromacs/bin/GMXRC
More info: after cmake successfully, during make I meet many warnings, one
of them like this:
/home/ooker/Desktop/gromacs-4.5.7/src/mdlib/forcerec.c: In function
'init_forcerec':
/home/ooker/Desktop/gromacs-4.5.7/src/mdlib/forcerec.c:288:15: warning:
'tmp_charge[3]' may be used uninitialized in
Dear all,
Is there any gromacs tool to project a given conformational change (i.e. the
structural difference after superposing a given protein in conformation 1 onto
conformation 2), on a set of already computed Principal components computed by
g_covar? Or should I implement myself ? I would
On 01.04.2014 21:10, Ly Minh Nhat wrote:
There is no output for source /usr/local/gromacs/bin/GMXRC
ooker@ooker-Aspire-4741:~$ source /usr/local/gromacs/bin/GMXRC
ooker@ooker-Aspire-4741:~$
There is GMXRC file in /usr/local/gromacs/bin.
Yes.
And after this 'source command', what does
$
g_anaeig
Cheers,
Tsjerk
On Tue, Apr 1, 2014 at 9:36 PM, Mendez Giraldez, Raul rmen...@email.unc.edu
wrote:
Dear all,
Is there any gromacs tool to project a given conformational change (i.e.
the structural difference after superposing a given protein in conformation
1 onto conformation
Hi Tsjerk,
Thanks for your answer, but g_anaeig (among other things) gives the
projection of each snaphot of my trajectory onto the selected PCs along
time. What I want is the projection of a different structure, for instance
the difference between my protein into a closed conformation (different
Hi Everyone,
I have a question about the implementation details of g_order. When I was
reading literatures, I found several interpretations of how the deuterium
order parameters are computed. One is calculate S_{ij} first, then
S_{CD} = \frac{2}{3} S_{xx} + \frac{1}{3} S_{yy}.
Another approach
I believe the two approaches you list are identical; the prefactors of 2/3
and 1/3 in the equation specified assume a tetrahedral symmetry. This
relation is often just stated as fact (since it is relatively
straightforward to derive) but there is a nice write up of it by J.-P.
Douliez, A.
thanks Justin,
in the Manual-5.0 i dont see the tool, i am assuming that the .itp file , is
generated by a tool similar as
genrestr as in older version??
Andrés Ortega
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On 4/1/14, 10:37 PM, Andres Ortega Guerrero wrote:
thanks Justin,
in the Manual-5.0 i dont see the tool, i am assuming that the .itp file , is
generated by a tool similar as
genrestr as in older version??
There's no separate too; it's just a different function type of the normal
Hi,
This happens due to pbc. You can use trajorder to get right structure.
Thanks.
On Tue, Apr 1, 2014 at 9:19 PM, sunyeping [via GROMACS]
ml-node+s5086n5015551...@n6.nabble.com wrote:
Dear all,
I am trying to visualize gromacs trajectory in VMD. when I load my .gro
file, the GUI window
Hi Raul,
The answer to a question with 'projection' and 'eigenvector' is g_anaeig.
But you project a structure, not a difference vector. You can also
calculate the inner product between two sets of eigenvectors, or between a
delta vector and a set of eigenvectors, again using g_anaeig (-inpr). I
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