*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*
COMMAND GIVEN :
[root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p
topol.top -pname NA -nname CL -nn 8*
:-) G R O M A C S (-:
On 31/03/2012 6:02 PM, oindrila das wrote:
*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*
COMMAND GIVEN :
[root@localhost gromacs-4.0.5]# genion -s ions.tpr -o
1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8*
Mark,
I've forced with some problems during MDrun of such system with the two
proteins.
Firstly, after addition of second protein, I've removed all water and ions
and solvated my system with genbox and genion.
Than I've redefined groups of my proteins ( wich are like a_1-4000 and
a_4001-5000 )
On Sat, 2012-03-31 at 15:46 +1100, Mark Abraham wrote:
On 31/03/2012 3:40 PM, Albert wrote:
Hi guys:
thank you very much for your kind comments. Probably the most
effective way is to optimize PME balance as Mark mentioned. It
seems that Mark's methods improved much much better for
On Sat, 2012-03-31 at 14:23 +0200, Dommert Florian wrote:
On Sat, 2012-03-31 at 15:46 +1100, Mark Abraham wrote:
On 31/03/2012 3:40 PM, Albert wrote:
Hi guys:
thank you very much for your kind comments. Probably the most
effective way is to optimize PME balance as Mark
James Starlight wrote:
Mark,
I've forced with some problems during MDrun of such system with the two
proteins.
Firstly, after addition of second protein, I've removed all water and
ions and solvated my system with genbox and genion.
Than I've redefined groups of my proteins ( wich are
rama david wrote:
Hi Gromacs Friends ,
I have 4 molecule system in water
Force field is G96 53a6 ..spc water molecule ..
How to find out relaxation time of my system ???
Relaxation time of what?
-Justin
All suggestion are welcome ..
I saved trajectory after 0.2 ps ..
Thank
Hello all,
Does anyone know where to look to do a slice of my unit cell along sections
(energies, forces etc...) or to just give a list of all atoms in the slice.
Something like an h,k,l or x,y,z slice through a section.
Stephan Watkins
--
NEU: FreePhone 3-fach-Flat mit kostenlosem
Justin,
I've minimised my system to emtool=1.0
but the error still occurs
31 марта 2012 г. 16:27 пользователь Justin A. Lemkul jalem...@vt.eduнаписал:
Separate COM motion removal groups are tricky. I'm still not completely
clear on what your system looks like, but if you've got two
James Starlight wrote:
Justin,
I've minimised my system to emtool=1.0
but the error still occurs
31 марта 2012 г. 16:27 пользователь Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu написал:
Separate COM motion removal groups are tricky. I'm still not
completely clear on
thank you very much for your kind comments. Probably the most
effective way is to optimize PME balance as Mark mentioned. It seems
The most effective way to get very quick simulations of the large
systems is to avoid PME
It is up to the researcher to ensure good accuracy anyway.
Dr.
Hi all,
I am just wondering about how GROMACS works when coupling temperature and
pressure.
Assuming the simplest coupling method, like Berendsen, does GROMACS just
scale down/ up kinetic energy (KE) for each particle in the system, such as
KE1/KE2 = T1/T2 ? Similarly for pressure, KE1/KE2 =
Hi all,
I' ve stumbled upon a problem when i used genion to prepare my files. Here's
the comand line:
genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq -1 -p
sistema.toI
I've got this in return:
Fatal error:
Your solvent group size (73282) is not a multiple of 19.
How to
Eduardo Oliveira wrote:
Hi all,
I' ve stumbled upon a problem when i used genion to prepare my files.
Here's the comand line:
genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq -1
-p sistema.toI
I've got this in return:
Fatal error:
Your solvent group size (73282) is
Hello all,
Does anyone know where to look to do a slice of my unit cell along sections
(energies, forces etc...) or to just give a list of all atoms in the slice.
Something like an h,k,l or x,y,z slice through a section.
Stephan Watkins
--
I believe the only way is to construct the
Eduardo Oliveira wrote:
First, thanks for the help!
Yeah i chose System. But, regardless my wrong choice, I still want to
know why does the solvent group need to be a multiple pf 19 or whatever
number for that matter. I searched in the gmx-users mailling list and
noticed that this is a
James Starlight wrote:
Justin,
31 марта 2012 г. 18:18 пользователь Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu написал:
Start by inspecting the initial configuration in the vicinity of
these atoms. Something is likely clashing here.
Yes, I've checked both of the
Justin,
Sorry that I can't provide you with such information now because that data
have been left in my lab workstation. Tomorrow I'll find all this logs and
attach it to this topic. Also I've run more properly CG minimisation (
EMtool=0.01) in double precission mode. I'll check this results too
On 2012-03-31 17:26, Dr. Vitaly V. Chaban wrote:
thank you very much for your kind comments. Probably the most
effective way is to optimize PME balance as Mark mentioned. It seems
The most effective way to get very quick simulations of the large
systems is to avoid PME
But you get
Hello:
I am trying to run g_tune_pme in blue gene with following script:
# @ job_name = bm
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.info
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 160:00:00
# @ notification = error
# @ job_type =
I believe that it's all described with reasonable detail in the manual.
Erik
31 mar 2012 kl. 18.42 skrev Yun Shi:
Hi all,
I am just wondering about how GROMACS works when coupling temperature and
pressure.
Assuming the simplest coupling method, like Berendsen, does GROMACS just
scale
On 1/04/2012 12:12 AM, lloyd riggs wrote:
Hello all,
Does anyone know where to look to do a slice of my unit cell along sections
(energies, forces etc...) or to just give a list of all atoms in the slice.
Something like an h,k,l or x,y,z slice through a section.
You can use g_select to
On 1/04/2012 4:50 AM, Albert wrote:
Hello:
I am trying to run g_tune_pme in blue gene with following script:
# @ job_name = bm
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.info
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 160:00:00
# @
On 1/04/2012 9:13 AM, Mark Abraham wrote:
On 1/04/2012 4:50 AM, Albert wrote:
Hello:
I am trying to run g_tune_pme in blue gene with following script:
# @ job_name = bm
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.info
# @ output = gromacs.out
# @ environment = COPY_ALL
Hi
Can gromacs use gromos forcefield file *.ifp? If so, could you please help
me how to use it. I cannot just add it to the topology files like adding
itp files. I searched the mailing list with no luck...
Thank you in advance !
Regards!
Eric
--
gmx-users mailing listgmx-users@gromacs.org
Dear All,
According to the lysozyme model in the tutorial of Justin Lemkul in
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html,
I am runing a 2 chain protein complex MD, and the steps are exactly same as in
that on-line tutorial except that I use the 2 chain
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