On Tue, Oct 9, 2012 at 12:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/9/12 12:21 PM, Ali Alizadeh wrote:
Dear All users
How to convert my single precision version of gromacs to double precision?
Is it possible?
You don't; you re-install Gromacs with the desired precision. Note
Hi Steven,
How much is 1 [pN/A] in [kJ/nm2] (without the mol)?
And why would anyone want to use force-constants in the 10^-23 ?
So why not define a force-constant for 1 mol of bonds instead of a sole bond?
I think you can see where I'm going.
Oliver
On Fri, Jun 29, 2012 at 2:32 AM, Steven
Hi,
as an alternative of applying position restraints to only the y-component,
one can also define a freeze-group only to act on the Y-axis by using:
freezedim N Y N
see: http://manual.gromacs.org/online/mdp_opt.html#neq freezegrps and freezedim
Oliver
On Fri, May 11, 2012 at 7:39 AM, Erik
Hi all,
This week Nvidia has also announced the GeForce GTX 690 with two
Kepler Chips [1].
That will make a total of 3072 CUDA cores @ 915MHz to 1019MHz and will
perform like two GTX 680s in SLI mode [2], but more energy efficient.
I'd really be interested if parallelization would be a
Hi Albert,
With the Information you give here, it's hard to give you specific
advice on how to speed up your simulations.
I found the following papers quite interesting and maybe they give you
some idea in how to improve the performance.
1. Larsson P, Hess B, Lindahl E (2011)
Algorithm
Hi Marc,
Though I never came across ready-to-use files for Gromos 45A4, you can
for sure get all the parameters for carbohydrates from [1] and
transfer them into a Gromacs format (make sure to convert all the
units).
Searching briefly for the term 45A4 in [2] lets me believe, that the
parameters
Hi Ahmet,
Let's imagine a sphere(two concentric spheres):
radius of the inside small sphere=rvdw
radius of the big sphere=rcoulomb
distance between two of our nested spheres:rlist
is this approach correct?
No. I suggest you read section 4.6.3 (and probably also 4.6.2) in the
Gromacs
A neat way to get generic coordinates of organic molecules like this
is using Jmol:
1) go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?USESIGNED
This requires Sun/Oracle Java plugin activated in the browser and
asks for permission to trust the signed applet.
Alternatively
Hi Stephan,
Have a look at:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
something like this should work:
--8--schnipp--8--
#!/bin/bash
for i in Temperature Pressure ; do
g_energy -f ener.edr -o ${i}.xvg EOF
${i}
EOF
done
Hi,
I recently came across the CELLmicrocosmos 2.2 MembraneEditor, in
which one can easily generate coordinates for mixed membranes and
AFAIK also insert a protein.
http://cm2.cellmicrocosmos.org/
http://pubs.acs.org/doi/abs/10.1021/ci1003619
I haven't had the chance/need to actually try it,
Dear Gromacs Community,
as I understand the MDP option continuation is the new name for the
option unconstrained_start.
I think the 4.5 series manual should be updated to mention that fact,
since it still only mentions unconstrained_start
(at least the html version of gromacs 4.5.1 :
in GLUH.
I found this in the ffoplsaa.rtp of gromacs 4.0.7 and as far as I can see
it's currently the same in the branches release-4-0-patches and
release-4-5-patches.
Cheers,
Oliver
--
Oliver Stueker
NRC - National Institute for Nanotechnology /
University of Alberta, Canada
--
gmx-users
Hi Hsin-Lin,
As Mark answered already yesterday:
1) 1Gb Ethernet is not fast enough for more than 2 or maximum 4 CPUs.
(and if each process of mdrun has to wait ~90% of the time to get data
from the others, then you result in just 10% load, right? )
2) telling from the line:
Hi Lum,
(Aside: Can you help with replying emails via this forum. I use gmail and
when I click the reply tab, it includes all the mails for that issue, and
there is no subject entry. So I always have to copy and paste the mail
before replying. I appreciate your help).
Even in Gmail you can
://www.gromacs.org/mailing_lists/users.php
--
Oliver Stueker
Post-doctoral Fellow, Bader Lab
Donnelly CCBR, University of Toronto, Canada
http://baderlab.org
phone: +1 (416) 978-0571
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
This email (as well as the two others) have found their way to the
list. No need to post several times!
On Wed, Mar 3, 2010 at 12:47, Gavin Melaugh gmelaug...@qub.ac.uk wrote:
Hi all
My apologies for the lack of detail in my previous e-mail. I am trying
to run gromacs-4.0.7 for a system
Hallo André,
Check the wiki:
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
Oliver
On Fri, Dec 18, 2009 at 10:59, Wojtyczka, André
a.wojtyc...@fz-juelich.de wrote:
Hi List,
is it possible to have the -merge option in pdb2gmx set to non-interactive?
I need to
Hi,
please someone correct me if I'm wrong,
but the equivalent of Gromacs 3.3.x :
pbc = full
is
pbc = xyz
periodic_molecules = yes
since Gromacs 4.0.
Oliver
http://manual.gromacs.org/current/online/mdp_opt.html#nl
On Thu, Dec 3, 2009 at 08:22, Eudes Fileti fil...@ufabc.edu.br wrote:
On 6/1/09 11:48 PM, Mark Abraham wrote:
Jinyao Wang wrote:
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
but I am getting the following the fatal error:
Fatal error:
Library file aminoacids.dat not found in current dir nor in
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