Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the concatenated trajectory.
I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a
different result, it means: if I take the first 10ps of my
Carla Jamous skrev 2010-10-15 12.05:
Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the concatenated
trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get
a different result, it
No, I don't think so because I did an .eps file (with xpm2ps) that indicates
the Time(ps) in x-axis and Hydrogen Bond Index in y-axis.
This is the way I'm reading my matrix.
Carla
On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund er...@xray.bmc.uu.sewrote:
Carla Jamous skrev 2010-10-15 12.05:
Yes, and it's the y-direction that is tricky. If I'm not mistaken, the
first row in the matrix is the *bottom* line in the graphical output.
Thus, the bottom line in the picture would be the first hbond in the
corresponding index file.
Erik
Carla Jamous skrev 2010-10-15 12.12:
No, I don't
Hi all,
I am using gmx4.5.1 g_enemat ,came across a error,
g_enemat -f pull.edr -groups -emat,
Opened pull.edr as single precision energy file
Will read groupnames from inputfile
Read 1 groups
group 0WARNING! could not find group (null):K-K (0,0)in energy file
Will select half-matrix of
Carla Jamous skrev 2010-10-15 12.05:
Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the concatenated
trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get
a different result, it
I'm sorry I don't understand, because your last answer doesn't correspond to
what's written in the manual. I'm using gromacs 4.0.3 and the manual says:
-hbm: existence matrix. Ordering is identical to that in -hbn index file.
And yes, my trajectory is concatenated the way I intended to, but I
The tricky part is that if you look at the first line in the file
hbm.xpm you are looking at the bottom row of the matrix when displayed
with gimp or after converting to xpm2ps. The same line corresponds to
the first hbond in hbn.ndx. That sentence in the manual is therefore a
bit ambiguous.
Stefane,
for more information on what Mark is talking about here, check out his
publication:
M. J. Abraham and J. E. Gready (2008) Ensuring Mixing Efficiency of
Replica-Exchange Molecular Dynamics Simulations J. Chem. Theory Comput.
(4), 1119-1128.
Dear all,
I come back to you for several
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On 10/15/2010 01:09 AM, Eudes Fileti wrote:
Dear Florian, thanks again.
I have worked with confined systems, where motion
in a given direction/plane is preferred. The accuracy of the MSD
approach for calculating the diffusion coefficient has
Has anybody checked g_hbond results for consistency between v4.0.7 and v4.5.1?
My usage is:
g_hbond -f my.xtc -r 0.68 -contact -life -s my.tpr -ac
and I find that the output files hbnum.xvg, hbac.xvg, hblife.xvg, and
the ac-reported lifetime of interactions are all different. To show
the
If I redo this, selecting only a single acceptor atom and 64 donor
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44
should have read 4 nm above. the point is that there really are 44
contacts, but v4.5.1 reports only 1.
contacts in one frame while v4.5.1 gives me only 1
chris.ne...@utoronto.ca skrev 2010-10-15 16.58:
If I redo this, selecting only a single acceptor atom and 64 donor
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44
should have read 4 nm above. the point is that there really are 44
contacts, but v4.5.1 reports only 1.
Dear users,
When I'm trying to create my solve box of 12x12x12 nm I encounter some trouble.
I'm using Gromacs 4.5 with the MARTINI force field to set up a system of 400
dipeptide molecules in water. However when I use genbox -cp coarse grained
dipeptidebox -cs MARTINI example water box -vdwd
Hi,
I found the following error when I tried to run xpm2ps.
*** glibc detected *** xpm2ps: realloc(): invalid pointer:
0x00dd0541 ***
=== Backtrace: =
/lib/libc.so.6[0x7f20a53b0dd6]
/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
xpm2ps(save_realloc+0x5e)[0x43741e]
Maurício Menegatti Rigo wrote:
Hi,
I found the following error when I tried to run xpm2ps.
*** glibc detected *** xpm2ps: realloc(): invalid pointer:
0x00dd0541 ***
=== Backtrace: =
/lib/libc.so.6[0x7f20a53b0dd6]
/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
Hi there,
I have installed the gromacs-4.5.1 and it was running without
problems. Also I installed the GPU version of GROMACS
(gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
NVIDIA driver are installed. Then I tried to run the test provided by
Alan with the mdrun-gpu and I
Hi,
Thank you for your answer. Unfortunately, I can't fix my problem.
I dont know if I'm doing this right, but first I type the line *git clone
git://git.gromacs.org/gromacs.git* in the command line. After all the
outputs, I tried to run xpm2ps again, but occured the same error.
2010/10/15
Maurício Menegatti Rigo wrote:
Hi,
Thank you for your answer. Unfortunately, I can't fix my problem.
I dont know if I'm doing this right, but first I type the line /git
clone git://git.gromacs.org/gromacs.git
http://git.gromacs.org/gromacs.git/ in the command line. After all
the
You should use the latest GROMACS version also for the GPU. Thus compile the
4.5.1 for the GPU and run this.
On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas renato...@gmail.com wrote:
Hi there,
I have installed the gromacs-4.5.1 and it was running without
problems. Also I installed the GPU
Hi Renato,
Fatal error:
reading tpx file (md.tpr) version 73 with version 71 program
This error occur because you are using different version of the gromacs.
Are you sure that the version of the grompp is the same of the mdrun
I hope this help.
Prof. Dr. Osmair V. Oliveira
Federal Institute
Hi,
I copy the file gmx_xpm2ps from the repository to my gromacs folder
/usl/local/gromacs/src/tools (i.e. I substitute the old file by the new
one). After that, I run xpm2ps and the problem persisted.
Any ideas?
PS: I run the same job in another i7, but with gromacs version 4.0.7
installed,
Maurício Menegatti Rigo wrote:
Hi,
I copy the file gmx_xpm2ps from the repository to my gromacs folder
/usl/local/gromacs/src/tools (i.e. I substitute the old file by the new
one). After that, I run xpm2ps and the problem persisted.
Any ideas?
As I said before, you have to actually
Hi gmx users:
I did normal mode analysis and got the hessian.mtx . Using the command
g_nmeig_d on the hessian.mtx
i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.
I need the complete eigenvector in the readable format. How i can get it?
Thank you.
with regards,
Rama
--
Postdoctoral
Hi everybody,
We're trying to understand how gromacs g_msd calculates MSD (without reading
through the C code, I really don't know much about it, and there are hundreds
of
lines).
(What we want to do is to calculate MSD properly in our supercooled water
simulations, i.e., to choose correctly
Hi,
Can anyone help to get the eigen vector in ascii format. I have with me the
trajectory file 'eigenvec.trr'.
On using g_covar_d, i got the the ascii format file 'covar.dat' and it has
covariance matrix of 3(NxN) number. But i am not interested in that.
I am interested in getting the
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