Thanks
On Tue, Jun 18, 2013 at 10:44 PM, massimo sandal deviceran...@gmail.comwrote:
2013/6/18 Hasni Arsad hasni.ar...@gmail.com
What should i do with this error massage:
Google it.
Program grompp, VERSION 4.6.2
Source code file:
Thanks,
Finally I managed to run MD of protein-ligand complex after a few trial of
tutorial
On Tue, Jun 18, 2013 at 5:06 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Please keep GROMACS usage questions on the gmx-users mailing list. Nobody
here is a private tutor :-)
The error
On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann s.neuman...@gmail.com
wrote:
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 5:16 AM, Steven Neumann wrote:
Thank
Hi,
you can use CAVER (http://www.caver.cz/) to detect tunnels. In the first
case you should not see anything while in the second you shold see a
channel.An other program you can use i s MDPocket ( '
http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/): It simply detects
cavities (either tunnels or
I will speak to someone who is familiar with the code. However, my Gromacs
version is installed on the cluster, can I create a file in my directory
which will use this code with a given potential?
On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann s.neuman...@gmail.comwrote:
On Tue, Jun 18,
On Wed, Jun 19, 2013 at 9:41 AM, Steven Neumann s.neuman...@gmail.com wrote:
On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann s.neuman...@gmail.com
wrote:
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul
No. You're modifying the C code, so you will have to learn to maintain
a GROMACS installation. Yet another reason to avoid modifying the C
code :-)
Mark
On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann s.neuman...@gmail.com wrote:
I will speak to someone who is familiar with the code. However,
Why? To avoid refining and extrapolating 100 tables for a Coarse grained
run and use constants instead... And to make it faster obviously.
On Wed, Jun 19, 2013 at 9:22 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
No. You're modifying the C code, so you will have to learn to maintain
a
Hello.
I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them give one and the same error:
Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal error:
Ab-initio calculation only
On 6/18/13 10:12 PM, Neha wrote:
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Please post a full .mdp file;
On 6/19/13 12:39 AM, Shima Arasteh wrote:
Do you mean the commands of inflateGRO controls the deletion radius?
Yes, that's its purpose. There is a published paper about its algorithm; I
would suggest you read and understand it.
The command which I use is what I got from tutorial:
On 6/19/13 6:11 AM, DavidPO wrote:
Hello.
I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them give one and the same error:
OK, good to know.
Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file:
Do you mean another published paper rather than published one in Methods
Journal? Another one which explains the algorithm?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday,
On 6/19/13 7:23 AM, Shima Arasteh wrote:
Do you mean another published paper rather than published one in Methods
Journal? Another one which explains the algorithm?
That's a useful one. There is a lot of helpful information on the InflateGRO
website
On 6/19/13 6:11 AM, DavidPO wrote:
Hello.
I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them give one and the same error:
Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal
Gromacs manual explains radial distribution function gAB (r, θ)
but g_rdf donot have options to directly do this.
Can anyone elaborate this.
--
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
--
gmx-users mailing listgmx-users@gromacs.org
On Wed, Jun 19, 2013 at 10:30 AM, Steven Neumann s.neuman...@gmail.comwrote:
Why? To avoid refining and extrapolating 100 tables for a Coarse grained
run and use constants instead...
I'd still think writing the script in your language of choice to write out
the tables is a much lighter weight
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit= 0.0
dt = 0.02
nsteps =
Dear all,
I found a paper where they have updated
the c36 forcefield to include cholesterol parameters ( to which I should be
able to modify by adding an oleate chain to get my cholesteryl oleate
moiety) :
http://pubs.acs.org/doi/pdf/10.1021/jp207925m
and I found this link:
Dear,
In the MD, I find that when the ligand keep in the active site , the
channel formed by two loops is closed. without the ligand the channel is
opened. I don't know how to describe the change of channel. could i describe
the channel by calculating the the most narrow distance(mass
I recently installed gromacs-4.5.5 and attempted to run the demo calculation.
I did not get new xterm windows opened and also get the following error:
Starting Trajectory viewer...
ngmx: Command not found.
[1] 23192
[1]Exit 1ngmx -f cpeptide_md -s cpeptide_md
I
On 6/19/13 9:25 AM, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit= 0.0
dt =
On 6/19/13 9:46 AM, Revthi Sanker wrote:
Dear all,
I found a paper where they have updated
the c36 forcefield to include cholesterol parameters ( to which I should be
able to modify by adding an oleate chain to get my cholesteryl oleate
moiety) :
On 6/19/13 11:21 AM, aixintiankong wrote:
Dear,
In the MD, I find that when the ligand keep in the active site , the
channel formed by two loops is closed. without the ligand the channel is
opened. I don't know how to describe the change of channel. could i describe
the channel by
On 6/19/13 11:26 AM, Raji Viswanathan wrote:
I recently installed gromacs-4.5.5 and attempted to run the demo calculation.
I did not get new xterm windows opened and also get the following error:
Starting Trajectory viewer...
ngmx: Command not found.
[1] 23192
[1]Exit 1
Please keep the discussion on the gmx-users mailing list.
On 6/19/13 12:14 PM, Raji Viswanathan wrote:
Dear Justin,
Thanks for your response regarding running demo with gromacs. Do I need to have
ngmx installed or can I use most functionalities of gromacs without installing
gromacs?
I
On 19.06.2013 15:25, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
dt = 0.02
Should be 0.03 according to S. Marrinks own remarks
(but wouldn't change your experience)
nstcomm
Addendum:
On 19.06.2013 23:16, Mirco Wahab wrote:
...
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water
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