Hi Justin and All,
The on-line document on Extending Simulations writes,
You might want to use the -append option of mdrun to append the new output to
the old files. Note that this will only work when the old output files have not
been modified by the user. Appending is the default behavior
On 4/04/2012 6:24 PM, Acoot Brett wrote:
Hi Justin and All,
The on-line document on Extending Simulations writes,
You might want to use the -append option of mdrun
http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun to
append the new output to the old files. Note that this will only
Hi all,
I recently started molecular dynamics with gromacs performing
protein-ligand simulations for my project first i worked out example from
justin tutorials on protein ligand system and trying to apply to my protein
and ligand.
First i generated topology for my protein using pdbgmx and then
Dear GROMACS users,
I'm a new user of GROMACS. The command mpirun -np 8 mdrun is working well
in a node with 8 processors.
Now I want to run GROMACS parallel on more processors, i.e., multiple
nodes. I tried to use mpirun -n 16 -host node018,node022 mdrun (node018
and node022 each has 8
Hello
If you add solvent water around your protein you have to generate a box with
the editconf command. How to know what shape that box should have? In my
tutorial is a dodecahedron used. What other boxes exist and how to know which
box one has to use?
Thanks
Greetings
Lara
--
gmx-users
Hello
I have a question about editing a pdb file.
I have a molecule in a box of water as a pdb file. I want to remove all water
except of ONE layer around he molecule. How to do that?
Do you know a software that is able to do that? Do you know how it could work
with programs like PyMol or
Hi Lara,
Please see editconf -h for the available box shapes. Which of these you use
is depending on your system (or a matter of taste actually).
The dodecahedron is mostly used to decrease the system volume, thus it's a good
choice for the simulation of a single protein in solvent (as in your
Hi
I have some problems to get do_dssp running:
I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using
gunzip dssp-2-linux-i386.gz. Next I copied it to the correct location: cp
dssp-2-linux-i386 /usr/local/bin/dssp and gave the user the right to
--- On Sun, 1/4/12, Ignacio Fernández Galván jel...@yahoo.com wrote:
Maybe instead of individual atoms, I should analyze the VACF
of the center of mass of each molecule, and the rotational
ACF. The latter I know how to do it. Is there an easy way
to calculate the former?
Silly me, I should
So if it were not quite clearly :)
my main question is about methodology of such gradually temperature rise
in the nvt enssemble conditions. Might it be realised by means of simple
equilibation in one mdp file varying some parametries to change time-step
of temperature growth? Or this
sai nitin wrote:
Hi all,
I recently started molecular dynamics with gromacs performing
protein-ligand simulations for my project first i worked out example
from justin tutorials on protein ligand system and trying to apply to my
protein and ligand.
First i generated topology for my
Rausch, Felix wrote:
Hi Lara,
Please see editconf -h for the available box shapes. Which of these you use
is depending on your system (or a matter of taste actually). The dodecahedron
is mostly used to decrease the system volume, thus it's a good choice for the
simulation of a single protein
Bernhard Knapp wrote:
Hi
I have some problems to get do_dssp running:
I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ .
Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied
it to the correct location: cp dssp-2-linux-i386 /usr/local/bin/dssp
and gave
James Starlight wrote:
So if it were not quite clearly :)
my main question is about methodology of such gradually temperature
rise in the nvt enssemble conditions. Might it be realised by means of
simple equilibation in one mdp file varying some parametries to change
time-step of
On 4/04/2012 10:02 PM, Justin A. Lemkul wrote:
Bernhard Knapp wrote:
Hi
I have some problems to get do_dssp running:
I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/
. Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I
copied it to the correct location: cp
On 4/04/2012 7:27 PM, Lara Bunte wrote:
Hello
I have a question about editing a pdb file.
I have a molecule in a box of water as a pdb file. I want to remove all water
except of ONE layer around he molecule. How to do that?
Do you know a software that is able to do that? Do you know how it
The problem with this solution is that I would have to recompile gromacs on all
maschines were I want to use dssp, right? Is there an older version of dssp
still available from somewhere? On the dssp-homepage I found unfortunatly only
the current but no past versions of dssp...
best,
Bernhard
Bernhard Knapp wrote:
The problem with this solution is that I would have to recompile gromacs
on all maschines were I want to use dssp, right? Is there an older
version of dssp still available from somewhere? On the dssp-homepage I
found unfortunatly only the current but no past versions of
Justin,thanks!
1) For example for the situation presented in manual for 2 groups with 3
and 4 points the time enty should be
annealing_time = 0 3 6 0 2 4 6
from this I've understood that 0 value is the start of timer for each group
and subsequent values are the actual time in the ps, havennt
James Starlight wrote:
Justin,thanks!
1) For example for the situation presented in manual for 2 groups with 3
and 4 points the time enty should be
annealing_time = 0 3 6 0 2 4 6
from this I've understood that 0 value is the start of timer for each
group and subsequent values are the
Justin,
1) I've defined 5 steps for specified definition of the time of each step
as well as for more flexibile controle of the such annealing: e.g I want
that equilibration step corresponded to the temperature between 320 and
330K will be longer than between first step corresponded to 300-310K
James Starlight wrote:
Justin,
1) I've defined 5 steps for specified definition of the time of each
step as well as for more flexibile controle of the such annealing: e.g I
want that equilibration step corresponded to the temperature between 320
and 330K will be longer than between first
On Apr 4, 2012, at 1:16 PM, Ignacio Fernández Galván jel...@yahoo.com wrote:
--- On Sun, 1/4/12, Ignacio Fernández Galván jel...@yahoo.com wrote:
Maybe instead of individual atoms, I should analyze the VACF
of the center of mass of each molecule, and the rotational
ACF. The latter I know
Hi,
I am trying to plot the ss content using the do_dssp command , but I am
getting the following error :-
Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0
/dev/null 2 /dev/null
I am using the DSSPold version. What could be the possible reason for such
an error ??
Dear All,
In the on-line tutorial on lysozyme
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html),
there is a command
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact
Will you please consider in that command whether
Dear All,
According to
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations , the
commands for extending MD are:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
But if you read
Dear All,
In http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf, there is a command
tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr –until $VALUE
But we know we never have the topol.tpr as I know.
Will you please give a clarification?
Cheers,
Acoot --
gmx-users
On 5/04/2012 1:58 PM, Acoot Brett wrote:
Dear All,
According to
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations; ,
the commands for extending MD are:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
But if you read
On 5/04/2012 2:07 PM, Acoot Brett wrote:
Dear All,
In http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf
http://www-personal.umich.edu/%7Eamadi/fwspidr_tutor.pdf, there is a
command
*tpbconv -f *traj.trr *-s *topol.tpr *-e *ener.edr *-o *tpxout.tpr
*--until *$VALUE
But we know we never
On 5/04/2012 10:25 AM, bharat gupta wrote:
Hi,
I am trying to plot the ss content using the do_dssp command , but I
am getting the following error :-
Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn
ddXN9mH0 /dev/null 2 /dev/null
I am using the DSSPold version. What could
Hi Gromacs friends,
When I given the command ...
pdb2gmx -f .. -o .. -p .. -ignh
I gate the following error..
--
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line:
1070
Fatal error:
atom N
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