This is what I mean by "quick and dirty".
#!/bin/bash
# Reads the output of "g_sas" per residue (-or) and writes only the residues
you want.
# Diego E.B. Gomes, Roberto D. Lins, Pedro G. Pascutti, Thereza A. Soares
# mailto: di...@biof.ufrj.br
#1 ) To perform multiple g_sas (will write out
There's a quick & dirty workaround. You can write a script to "g_sas" each
frame individually, writing many output files. Then grab the results from there.
Sent from my iPhone
On Jul 7, 2011, at 9:17 PM, "Justin A. Lemkul" wrote:
>
>
> ahmet yıldırım wrote:
>> There are hydrophilic and hydr
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get gromacs 4.04
Confirm if you changed the permissions correctly and can write
anywhere in /usr/local/
Are you doing this as 'root' or super user (sudo) ? Because if you
are just a regular user, will won't be able to change the permissions
in /usr/local/. So, configure gmx to be install
Did you download the "dssp" software from here ?
http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
On Mar 10, 2009, at 1:12 AM, Homa Azizian wrote:
Hi
when I use do_dssp the following error come:
Program do_dssp, VERSION 4.0.3
Source code file: do_dssp.c, line: 471
Fatal error:
Failed to execu
You mean that half the protein is in one side of your cubic box and
the other half is on the other side ?
Try removing PBC or fitting to a reference frame (like the one before
SA). Search the list archives, this is a very common question.
On Mar 9, 2009, at 10:17 PM, Homa Azizian wrote:
I
Diego.
--
=====
Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA. +1 (509) 372.6363
diegoenry.go...@pnl.gov
=
On Mar 10, 2009, at 12:36 AM, Andrew Voronkov wrote:
Dear GROMACS users,
I'm doing
uot; test to check if MPI compilation worked.
% which mdrun_mpi (find where mdrun was installed, mine is at /usr/
local/gmx4/bin/)
% ldd /usr/local/gmx4/bin/mdrun_mpi
You should see "libmpi.so.0" in the list of libraries, if not, go back
to the ./configure step.
Diego
--
====
ou job finishes you might want to stop the mpi daemon by running:
mpdallexit
Diego.
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=====
Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA. +1 (509) 372.636
These results are not strange.
Performance results really depend on the size/setup of your system.
Next time use gmxbench so we can have a better reference.
Are you using gromacs 4.0.4 ? It scales much better than gromacs-3.x.x
versions. Anyway, this very bad scaling is normal over gigabit
Check the VMD list, you should find the script there.
On Feb 1, 2009, at 9:28 PM, Mark Abraham wrote:
nahren manuel wrote:
Dear Gromacs Users,
I have done PCA of my MD , I want to visually represent the motions
in terms of porcupine plots. I came across Dynamite (web server)
for this purpo
********
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
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Lab
-s md.tpr -f md.nojump.xtc -o md.nojump.fit.xtc -fit rot+trans
4) check the result with "vmd", it looks beautiful
5) g_rms -f md.nojump.fit.xtc .
Have fun,
Diego Enry.
On Wed, Jun 18, 2008 at 2:55 AM, Yang Ye <[EMAIL PROTECTED]> wrote:
> Quite likely, it is due to part of molecul
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make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
> make: *** [install-recursive] Error 1
> I have try to edit the end of the configure command "/usr/local/gromacs332"
> with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue
&
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Ethernet has very high latency, it wasn't made for this kind of thing.
Gmx 4 will be much much better, check the paper gromacs website.
On 3/6/08, Ricardo Soares <[EMAIL PROTECTED]> wrote:
>
> Diego Enry wrote:
> On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EM
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ul to you. I have only one question. How can I configure mpi/lam
> for relaize the comunication between nodes?
> I have created an hostsfile with my ip addresses.
> Thank's a lot in advance.
>
> Mario
>
> Diego Enry <[EMAIL PROTECTED]> ha scritto:
>
> Since
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I think I saw this before... check if openmotif contains this library
and install it or just try.
./configure --without-x --enable-mpi
Cheers,
Diego Enry.
On Jan 18, 2008 6:45 AM, Andreas Kukol <[EMAIL PROTECTED]> wrote:
> On SuseLinux 10.3 the command ./configure --enable-mpi works
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Please check the FAQ & list achives b4 posting. Your answer is already there.
Is there any smart way to continue a run that crashed?
http://www.gromacs.org/content/view/62/29/
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Br
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> 3.3.1/man/man1/g_nmens.1'
> /usr/bin/install: `./g_nmens.1' and
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_nmens.1'
> are the same file
> /usr/bin/install -c -m 644 './g_tcaf.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/
TECTED]
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Diego Enry wrote:
> 4 months later... I´m having the same futil.c File input/output error
> with a brand new instalation. root also works fine for me.
> Hernan how did you solve it ?
On 10/20/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
still the same unix/linux probl
, not also to
gmx-users-request.
Thanks,
Mark
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Laboratório de Modelagem e Dinamica Molecular
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)
The big concern is how to deal with a net charge of almost "-250" ?
(guide me DNA guys)
1) Should I add a huge amount Na+ as counter ions ? Randomly ?
2) And what about long-range electrostatics ? PME would be fine, or
should I try Reaction-Field ?
Thanks,
--
Diego Enry B. Gomes
;-250" ?
(guide me DNA guys)
1) Should I add a huge amount Na+ as counterions ? Randomly ?
2) And what about long-range electrostatics ? PME would be fine, or
should I try Reaction-Field ?
Thanks,
--
Diego Enry B. Gomes
@ Pacific Northwest National Laboratory.
Laboratório de Modelagem e Dinamica
Hi Yuguang,
you don't have to wait your mdrun job to finish to check out your
energies,trajectories.
Just use "g_energy" and you'll get the energies up to the last frame
wrote on .edr file.
Diego Enry.
On 8/4/06, Mu Yuguang (Dr) <[EMAIL PROTECTED]> wrote:
Dear all,
Hi list,
I couldn't find in the archives and "3.2 to 3.3 changes" what happened
to "-g" flag in g_hbond ?
Is the old "hbond.log" information written somewhere else ?
Diego Enry.
// command line
g_hbond_331i -g(intel compiled)
// error message:
Program
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