10 ps is too short of a trajectory, even for such a large system (for pure
water it is considered large). i would guess that it is a typing-error and
you ran for 10 ns?
omer.
On Wed, Feb 10, 2010 at 11:05, Amit Choubey kgp.a...@gmail.com wrote:
I use a box of volume 6x6x6 nm^3 which has 7161
See for example eq. 19 20 at JCP 129, 84505 (
http://dx.doi.org/10.1063/1.2968608). Is this what you meant?
Omer.
On Mon, Dec 14, 2009 at 06:56, Mark Abraham mark.abra...@anu.edu.au wrote:
I think that the problem comes from pbc handling for molecules splited
across boundaries - I expect : do
Maybe the system is exploding? Have you looked at the movie?
And I agree with you that it might be unrealistic to do simulation at 600K
using a force-field which was parametrized at 300K.
Omer.
On Thu, Nov 26, 2009 at 05:56, Neha Bharat Gajaria n.gandh...@gmail.comwrote:
Dear List,
I m
On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek ondrej.marsa...@gmail.comwrote:
Dear all,
I would like to understand better the way g_rdf performs
normalization. I have two unexpected results:
1) In a simple simulation of atomic ions in water in a cubic box, I
get RDFs that clearly reach a
On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin chihying2...@gmail.com wrote:
So, how can I remove the periodic boundary condition to get the truly
movement of the atoms between the two time steps ?
Removing PBC and placing atoms back into their true location is easy. In
general, if an atom has
Is the decrease occurs in the long times? Omer.
On Tue, Nov 17, 2009 at 21:08, Chih-Ying Lin chihying2...@gmail.com wrote:
HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I
simulate the protein and ligand system and then calculate the MSD of the
ligand. Then, i drew
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren ch...@nus.edu.sg wrote:
Ahh, now I understand - sorry, Omer!
No problem, glad to help.
In fact, I have compared all three single hydrogen RDFs and they are
identical and also relatively smooth. Since, however, with 3 times more data
points
of the hydrogen bond, for example.
If you are unsure of your g(r) calc it just for water (that is - only
oxygen-oxygen of water-water). At long distances (~10 Angstroms) it should
fluctuate around 1.
Bests, Omer Markovitch.
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On Sat, Oct 17, 2009 at 06:10, lammps lammps lammp2fo...@gmail.com wrote:
Dear,
I want to do stochastic simulations in the framework of Langevin dynamics
using Gromacs with the reduced units. The questions are:
1. How to turn on the reduced units? Is there any parameters for setting?
I
Have you tried:
echo 0 zero
trjconv bla bla bla zero
You could put more arguments in the file, for example - use the -center
option, and then echo another 0 into the zero file.
--Omer.
On Sun, Oct 4, 2009 at 18:22, ABEL Stephane 175950 stephane.a...@cea.frwrote:
Dear GMX Users,
echo
For VMD you first load a GRO (or pdb) file, and then XTC.
The XTC file should contain _exactly_ the same number of atoms as the GRO
file. Did you save the entire system in the XTC, or just a specific part of
it?
Omer.
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
Work with groups and an index file, and define energy_groups in the mdp file
also.
For indices, check make_ndx utility.
Omer.
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Fri, Oct 2, 2009 at 20:31, Pradip
If you are performing LD then setting ldseef=-1 does the trick. For MD, try
genseed as suggested. I believe the manual explains all, including the
range issue.
Omer.
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On
Trj trjconv -pbc nojump, or trjconv -h and read the short help printed.
Omer.
I actually didnt realize this until i did a long simulation after which the
trajectories of some of the atoms looked way out of the box dimensions. The
co-ordinates of many atoms didnt lie in the box range.
How do you run vmd?
The first argument should be a GRO or PDB file, and the second argument is
the TRR or XTC trajectory.
Alternatively, you can open a new molecule in vmd and than load data into
that molecule.
--Omer.
On Thu, Sep 24, 2009 at 08:21, Aditi Borkar aditi.bor...@gmail.com wrote:
I assume that atoms from opposite ends of the simulation box are being seen
by GROMACS as being 1-4 neighbors as a result of the PBC,
Are you sure? have you looked at the last good frame before this message?
GMX treats PBC as it should during MD neighbour search, so maybe this is a
pair that
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its
total kinetic energy fluctuates more.
--Omer.
On Wed, Sep 16, 2009 at 12:10, Stephane Abel stephane.a...@cea.fr wrote:
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.4 0.4 ; time constant,
Thanks Mark.
I am simulating a dimer in vacuum, and it is my understanding that once a
non-bonded interaction has exceeded the table-extension cutoff this
interaction will NOT be included in the potential for the remaining
simulation, even if it will later come back to a distance within the
Thanks.
And what happens if later on it comes back to the cut-off + table-extension
range?
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Thu, Aug 27, 2009 at 11:13, Berk Hess g...@hotmail.com wrote:
A
But what if the gmx code did notice it?
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Thu, Aug 27, 2009 at 16:21, Mark Abraham mark.abra...@anu.edu.au wrote:
It would look up a non-random energy and force. If
Dear GMXs,
I would like to clear something out, for myself:
The table extension given in MDP file applies to nonbond_params pairs
interactions which are specified in the TOP file (and also electrostatics)?
Is there an interaction which does not use the table extension (other then
bonds, angles
Try combining indices with that, use make_ndx -h. --Omer.
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Wed, Jul 22, 2009 at 18:27, Justin A. Lemkul jalem...@vt.edu wrote:
The trjconv -pbc options were
Try using trjconv. Look at the -pbc options and also maybe -center options.
--Omer.
Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Wed, Jul 15, 2009 at 10:09, nikhil damle pdnik...@yahoo.co.in wrote:
but
Dear All,
I would like to ask your help on the following - I want my simulation to
include a surface, and have PBC.
The surface I chose is aligned on the XY plane. However, the surface is not
a square.
The surface dimensions are a=b=169.2 c=6.9 Angstroms, the angles are:
bc=ac=90 ab=120 degrees.
I prefer to keep discussions professional, Mark and Tsjerk.
Anyway, I am doing MD with PBC. I have a surface which sits on the XY axes,
the surface is not a square and my question is how do I tell gromacs that I
have a non standard box. Please see my original post for more details:
++
I
Remember that for PBC=xyz, the neighbor search is faster, so I suggest using
PBC with a very large box.
--Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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How many letters for residue name are allowed in the PDB format? Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Hello Osmair,
Perhaps you can try using the [ nonbond_params ] [ pairs ] sections of
the TOP file?
How did you define these interactions in your TOP file?
--Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Fri, Apr 17, 2009 at
Hello.
What do you mean by jump? Perhaps the connected MN is a stable state?
If you'll supply more details we could try to help you better.
--Omer.
On Sat, Mar 14, 2009 at 08:15, Homa Azizian haziz...@razi.tums.ac.irwrote:
My ion jump out of the protein after MD.My ion (MN) has not any covalant
, that is- by the Langivin thermostat.
With MD, the thermostat works like friction (positive or negative friction).
So you see, that for LD, an initial velocity of zero should next be changed
by the thermostat, while for MD the rescaling shouldn't work for zero.
--Omer Markovitch.
Koby Levy research group
Use: trjconv -f conf.gro -s conf.gro -o conf.pdb.
Note the use of -s on the same gro file.
--Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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See also the work of Hummer (JPC-B (2004),
http://dx.doi.org/10.1021/jp0477147), dealing with box size effect on D.
Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Tue, Mar 3, 2009 at 23:37, Eudes Fileti fil...@ufabc.edu.br
Why not create dummy topologies, without charges/vdw ?
Another option, which I am not sure of its effect, is, perhaps, to take
extremely small cutoffs.
--Omer.
Lee Soin wrote:
I'm trying to rule out the effect of electrostatic or Van der Waals
interactions while performing a simulation. Do
, the speed of the expansion changes but all
simulation converged to a small density between 50-100 kg/m3.
Your help is appreciated; Probably, I am not controlling the simulation like
I should. I will appreciate any advice.
Thank you, Omer Markovitch.
I have used gromacs version 3.3.3, Here is my .MDP file
Also check out make_ndx -help. Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Mon, Jan 19, 2009 at 18:28, Vitaly Chaban vvcha...@gmail.com wrote:
I am running a simulation of 5 time steps and am trying to avoid
setting
would you please tell me for compare dynamic peptide what time for MD
is enough by gromacs?generally.
You can take your 20 ns simulation, and divide it into 2-4 parts, each 10
(or 5) ns long.
Then, calculate the property you are interested in for each part seperately.
If 20 ns is more then
Supposed I have a .gro file of 38 molecules of A which are already in
equilibrated conformations. Now I want to transform 15 molecules of A into B
therefore I will have the binary mixture of A/B with 13:15 molar ratio in
the final structure. How can I do this? Any suggestions will be
On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty
[EMAIL PROTECTED]wrote:
Dear all,
I have a very long trajectory split over a large number of files. What
would be the most efficient way to use the analysis programs over them?
Do they support multiple input for trajectory? Or I need to
Dear,
I am simulating a small protein (less then 50 amino acids) at room
temperature, with no additional atoms and/or molecules and/or ions. The
simulations seems to proceed ok (in terms of avg. kinetic energy and other
energy terms).
Then, I take the same protein, and introduce a surface to the
On Mon, Nov 10, 2008 at 17:42, Seunghyun Chung [EMAIL PROTECTED] wrote:
Deal all,
Is there any practical approach to choose the right temperature coupling
strength for a simulation? For example, if a system behaves differently with
weak coupling and strong coupling, which result I should
Dear All,
I am trying to perform Langevin dynamics of large peptides / proteins.
After reading the manual going over some old mails in this list, I have
two points I hope you could clear for me:
[Gromacs version 3.3.3]
1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the
Thanks for the quick reply Berk.
1) Is this the proper keywords I should use for Langevin dynamics:
integrator = sd ;
bd-fric= 0 ;
tau_t = 10 ;
ref_t = 300 ;
Basically, I want to know if I am using the 4 parameters correctly.
That is - for Langevin dynamics, I should pick
I believe that (-1) as the seed takes the time or something as the actual
seed, thus ensuring no two identical seeds, and no two identical velocities.
Omer.
On Fri, Oct 17, 2008 at 12:11, sarbani chattopadhyay
[EMAIL PROTECTED] wrote:
I want to know that does this ensure that the mdrun
In short - you can apply PBC in all directions (XYZ) by choosing the proper
keyword in the .mdp file, I believe the box dimensions are defined in .gro
file.
Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Fri, Oct 10, 2008 at
Oh, I didn't read carefully.
My suggestion would be, perhaps, to physically put atoms on the sides of the
box (possibly, fill each side completely), and to place on them very high
repulsion.
You might want to freeze them up, and exclude their self interactions from
the energy calculation.
Good
Boundary should not precisely be around the protein, otherwise some parts
of the protein would feel other parts via the boundary.
In general, if you apply periodic boundary conditions (PBC), take the
dimensions as such so the protein would NOT feel the PBC.
Say you have an unfolded protein (or a
Hello,
I have ran some MD with GROMACS v3.3.3, and used the command trjconv -f
traj.xtc -o traj.pdb -s file.gro to generate a pdb movie.
My simulation includes charged atoms in some residues, but the output pdb
does not seem to include the formal charge data.
My question is, is this a known issue
of the water dimer.
For example - what causes the activation energies of the forward backward
rate constants to be about similar rather then being different by the
strength of 1 HB?
Hope I was clear.
Omer Markovitch.
** a link to JCP 129, 84505 (2008) http://dx.doi.org/10.1063/1.2968608
Please see also my reply under HB lifetime to Christopher Daub.
I think that JCP 129, 84505 (2008) should be read when dealing with C(t) in
general HB lifetimes in particular.
** link: http://dx.doi.org/10.1063/1.2968608
Omer Markovitch.
___
gmx-users
electrostatics here:
1) As is, and letting the two oxygens repel one another.
2) Ignore this specific pair when calculating?
How does GROMACS operates? I think that (1) is the common practice, but I
want to be sure.
Thank you, Omer Markovitch.
(this email was sent to gmx-dev. by mistake)
Koby Levy
There is no non-bonded interaction between these two oxygens, unless you
are using an Urey-Bradley potential for the angle, like in the CHARMM force
field. Most (if not all) of the standard force fields in Gromacs treat the
interaction of these oxygens within an angle definition, which is a
Shalom,
Is it just me or there is a bug in the archives search page
http://www.gromacs.org/search ?
(error 404 - page not found)
--omer.
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search
it
large enough so the computation would be feasible.
Other then that, look at the previous answers you got for a more hands on
approach. You might also want to read about integrating MD.
--Omer Markovitch.
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has healing powers.
Please refer to the gromacs manual for more details, and to the gromacs wiki
aswell.
Omer Markovitch.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Thu, Sep 18, 2008 at 12:03, Christopher Ambe [EMAIL PROTECTED]wrote
What is the reason for shrinking the box?
If it is for technical reasons, for example - nicer visualization etc`, then
perhaps this could be done manually.
If you plan to use the smaller box later, then maybe you could do some part
of high pressure simulation, to reduce box size while keeping it
not understand how to do it and in
which files.
Thank you, Omer Markovitch.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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http://www.gromacs.org/mailman
Thank you both! Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Sat, Sep 13, 2008 at 15:57, Justin A. Lemkul [EMAIL PROTECTED] wrote:
Omer Markovitch wrote:
Hello,
I would like to ask for your help in defining groups
Using emails, this might be done manually - each user will add to the
TOPIC something like: tag install, etc`.
Then each user could define his own rule, in his personal email account, how
to deal with messages that contain tag xxx gromacs in the topic.
Just a thought... Omer.
Koby Levy research
Are you sure this will be done automaticaly if you'll procide gromacs with
an output file called filename.trj?
There is also the option of converting into PDB: trjconv -f traj.xtc -o
trajtraj.pdb -s coordinates.gro.
omer.
Koby Levy research group,
Weizmann Institute of Science.
to me too.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Mon, Sep 8, 2008 at 16:30, Vitaly Chaban [EMAIL PROTECTED]wrote:
gurgo If anyone has a simpler example along the lines of my interests,
gurgo please send me it!
and to
Regarding buildit FFT - I believe they say it is slower then other packages.
Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Thu, Sep 4, 2008 at 21:54, Myunggi Yi [EMAIL PROTECTED] wrote:
I have done the compilation.
Thank
:
Omer Markovitch wrote:
Dear All,
I would like to consult you on the following two things:
1) I have a small, preanalysis, routine I would like to run each time a
frame is written and added to the trajectory file.
After some checking, I believe that, in the file *stat.c*, the routine
Dear All,
I would like to consult you on the following two things:
1) I have a small, preanalysis, routine I would like to run each time a
frame is written and added to the trajectory file.
After some checking, I believe that, in the file *stat.c*, the routine
*void write_xtc_traj(FILE
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