On Sat, 2012-06-09 at 15:33 -0700, Mr Bernard Ramos wrote:
Hi everyone!
I have a 20 ns simulation (2fs timestep but coordinates saved every
0.2 ps) and I was able to calculate the mean-square-displacement of
the oxygen atoms of my water solvent. The entire MSD plot looks very
linear to
On Sun, 2012-06-03 at 10:47 +0200, Erik Marklund wrote:
I once took this course in Amsterdam and can highly recommend it:
http://molsim.chem.uva.nl/molsim2012/index.html
Me too. Almost all of the PhD students, who join the group where I am
currently working in, go there and so far everbody
On Fri, 2012-06-01 at 18:09 +0200, Erik Lindahl wrote:
Hi,
First: Let me thank each and every one of you who took the trouble to fill
out our user survey. The resulting information is invaluable to us, and Mark
Berger of NVIDIA has been a tremendous help in assembling the results and
Hi,
I do not know, how TIP4P/2005 has been parametrized, but the VdW cutoff
you are using is quite large. Did the authors of TIP4P/2005 really
applied this large cutoff ? This is very important, because the force
field is always parameterised in respect to certain parameters and vdW
is an
On Fri, 2012-05-18 at 09:49 -0700, Milinda Samaraweera wrote:
Hi Guys
Could you please explain to me how to use the g_dipole method to
calculate the dipole moment of a Solute in a solvent.
Hi,
there has just recently been a discussion on this mailing list. Actually
you need just an
On Tue, 2012-05-15 at 19:47 +0100, Lara Bunte wrote:
Hello
To make better energy minimization procedures I read about thermostats and
barostats. I understand the physical concepts and differences between global
and local thermostats and the difference between Berendsen and Nose-Hoover
Hi Tsjerk,
sorry for the strong statement. I should have said:
should be applied ...
instead of
only applicable.
You are right, the question is how big is the difference and actually
one would also expect, that the differences vanish with 1/N. However, so
far it is unknown, what kind of
On Tue, 2012-05-15 at 09:17 +0100, David de Sancho wrote:
Dear all
I have been following Justin Lemkul's tutorial for the lysozyme
simulations
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
I am using Gromacs 4.5.5.
Compiled in double or single
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote:
Hi,
You do not need to use the polarizable martini water model to
calculate the dipole of molecules. Or I am missing a point here!
g_dipole should do the work
XAvier.
Hi,
I want to point to another problem. If you
On Mon, 2012-05-14 at 11:55 +0200, Bala subramanian wrote:
Dear gmx-users, I have some doubts on the manual pages. Kindly help to
understand the same.
Section 5.7.1 Page 129
1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not
present in the pair list from normal
://pubs.acs.org/doi/abs/10.1021/ct200375v
while the theory is based on:
http://dx.doi.org/10.1063/1.3060164
and applied to water in:
http://pubs.acs.org/doi/abs/10.1021/ct1002048
/Flo
XAvier.
On May 14, 2012, at 12:01 PM, Dommert Florian wrote:
On Mon, 2012-05-14 at 09:59 +0200, XAvier
On Fri, 2012-05-11 at 10:23 +0200, Bernhard Knapp wrote:
Dear gromacs users
In a recent paper I found the following protocol of a gromacs simulation:
All simulations were performed with the GROMACS 4.0 [12] compiled in
single-precision mode at a constant temperature of 277 K in a
On Tue, 2012-05-08 at 11:38 -0700, Milinda Samaraweera wrote:
Hi Guys
I was using the program http://q4md-forcefieldtools.org/RED/ to
derrive ESP based charges for some molecules that I study. Is this a
correct method to do so if not please let me know what are the other
methods that are
Hi,
it is the ionic current, given by a sum over the center of mass
velocities of each molecule by their net-charge.
/Flo
On Mon, 2012-05-07 at 13:00 -0400, Andrew DeYoung wrote:
Hi,
g_current calculates the (ionic) current in the output file specified by the
-o switch (by default,
On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote:
Interesting discussion indeed. I'm just thinking that there might be
no fundamental difference to other thermostats. There's nothing in the
way that causes the friction, but then again, there's no physical
particle that causes the
On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote:
Hi Florian,
I remark that Langevin method is used also for explicit water system!
But there a big question arises to me. The thermostatting by Langevin is
achieved due to random kicks. If I simulate all atoms explicitly, there
On Fri, 2012-05-04 at 11:07 +0200, Erik Marklund wrote:
4 maj 2012 kl. 10.45 skrev Dommert Florian:
On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote:
Hi Florian,
I remark that Langevin method is used also for explicit water
system!
But there a big question
Salam,
man yekam Farsi fahmam, amma only in Penglish ;) However, perhaps you
try English and get more response.
Khodafes,
Flo
On Fri, 2012-05-04 at 04:50 -0700, Hengameh Fallah wrote:
Gromacs? نقاشی؟ :)
On 5/2/12, leila separdar separdar.le...@gmail.com wrote:
salam,
man
On Thu, 2012-05-03 at 07:32 +0200, Albert wrote:
hello:
I wondering are the three thermostat methods: Langevin, Berendsen
and Nose-Hoover chain are all compatible with semi-isotropy coupling
style? If I would like to use semi-isotropy coupling method, which one
would be better?
thank
On Thu, 2012-05-03 at 10:45 +0200, Albert wrote:
Hello Flo:
thank you so much for your kind comments.
Yes, I would like to couple the pressure, it really helps a lot.
best
Albert
You're welcome. There is just one little typo
On 05/03/2012 10:40 AM, Dommert Florian wrote
On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote:
Hello,
2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de
On Thu, 2012-05-03 at 07:32 +0200, Albert wrote:
hello:
I wondering are the three thermostat methods: Langevin,
Berendsen
On Thu, 2012-05-03 at 11:31 +0200, francesco oteri wrote:
2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de
On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote:
Hello,
2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de
On Mon, 2012-04-30 at 13:49 -0400, Andrew DeYoung wrote:
Hi,
Is it possible to compute the ion conductivity using any of the existing
Gromacs tools? Ion conductivity is proportional to the current-current
(auto)correlation function.
For example, the current J_z(t) along z can be
On Mon, 2012-04-23 at 12:41 -0400, Justin A. Lemkul wrote:
On 4/23/12 11:36 AM, Bala subramanian wrote:
Friends,
I have created the top (attached) file for a tripeptide using pdb2gmx tool
of
gromacs. However in the top file, i dnt see the pdb2gmx writing the ff
parameters.
I
On Fri, 2012-04-20 at 10:33 -0400, Andrew DeYoung wrote:
Hi,
I am wondering how the fourierspacing parameter corresponds to fourier_nx,
fourier_ny, and fourier_nz. The manual
(http://manual.gromacs.org/current/online/mdp_opt.html#ewald) says, For
ordinary Ewald the spacing times the box
On Fri, 2012-04-20 at 11:35 -0400, Andrew DeYoung wrote:
Hi Florian and Mark,
Thank you for your time!
I am actually using (fourier_nx, fourier_ny, fourier_nz) ~ (14, 14, 125).
This is what a colleague who has recommended, although she is using a
different (somewhat slower) MD package.
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
On Tue, 2012-03-20 at 11:38 +0200, Ioannis Beis wrote:
Message: 3
Date: Mon, 19 Mar 2012 15:05:43 +0100
From: Dommert Florian domm...@icp.uni-stuttgart.de
Subject: Re: [gmx-users] g_msd with input by trjconv -pbc nojump:a
concern
To: Discussion list for GROMACS users gmx-users
Hello,
there are several ion non-bonded ion parameters provided in the OPLS-AA
files of Gromacs, and the reference from an article Jorgensen et al.
from 2001. However I was not able to find the corresponding atom types
in this article and so far also not in any other article of the OPLS-AA
La3+, given in GROMACS, are not provided
unfortunately.
/Flo
Dommert Florian wrote:
Hello,
there are several ion non-bonded ion parameters provided in the OPLS-AA
files of Gromacs, and the reference from an article Jorgensen et al.
from 2001. However I was not able to find
Hi,
perhaps this problem is related to bug 774:
http://redmine.gromacs.org/issues/774
which has been discussed quite often, recently. Somehow there is a
problem in the order of removing the PBC and jumps. As already
mentioned, I could solve the problem by providing a trajectory with
whole
On Wed, 2012-03-07 at 12:33 +, Lara Bunte wrote:
Hi
After I used
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
to collect my files into one em.tpr file (which is the meaning of gromp as
fas as I understand it)
Then I start mdrun for energy minimization with the
On Mon, 2012-03-05 at 23:56 +1100, Mark Abraham wrote:
On 5/03/2012 11:39 PM, Gavin Melaugh wrote:
Dear All
I have a system of 40 solute molecules in 480 crown ether solvent molecules.
When I ran the msd analysis on the solvent molecules using the following
comand.
g_msd_login_d -f
. If you use this force field, how are the other parameters
obtained ? Are they zero or do they correspond to the OPLS values given
in the reference cited on the top of the table ?
/Flo
On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian
domm...@icp.uni-stuttgart.de wrote:
On Fri, 2012-02-24
is an artefact of low
accuracy.
/Flo
On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian
domm...@icp.uni-stuttgart.de wrote:
On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote:
The ionic liquid is bistriflate N-methyl-N-propyl
pyrrolidinium and
the force field
gen_seed= -1
On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian
domm...@icp.uni-stuttgart.de wrote:
On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:
Dear all,
I am trying to equilibrate a solvent of pure ionic liquid.
The system
On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:
Dear all,
I am trying to equilibrate a solvent of pure ionic liquid. The system
keeps exploding (after 2-5 ns) and I am not sure why, though I believe
coulombic interactions are to blame. This is because the Coul-SR term
is negative, but
On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote:
Just one last question Tsjerk, I was trying to load the cg.gro file
obtained with martinize in vmd and the program says it is unable to
load the molecule. the result of the martinize script looks like:
MODEL1
TITLE
On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote:
Hi,
I was wondering whether BD simulation integrator in Gromacs also
have option of including hydrodynamic interactions.
Hello,
I do not think, that Gromacs has something like Lattice-Boltzmann
implemented so far. Furthermore you would need
Forwarded Message
From: Sanku M msank...@yahoo.com
Reply-to: Sanku M msank...@yahoo.com
To: Dommert Florian domm...@icp.uni-stuttgart.de
Subject: Re: [gmx-users] BD with Hydrodynamic interactions?
Date: Mon, 26 Sep 2011 04:07:38 -0700 (PDT)
I did not mean lattice boltzmann
On Sun, 2011-09-25 at 15:49 +0300, Ehud Schreiber wrote:
Hi again,
Quoting from the current Gromacs GPUs webpage:
Force Fields: Supported FF are Amber, CHARMM. GROMOS and OPLS-AA are not
supported.
Hello,
if read the line above correctly, there is a full-stop after CHARMM.
Hence it
On Mon, 2011-09-12 at 21:57 +0530, chandran karunakaran wrote:
Hi Gmx users,
Are we able to run both the lower and higher version at a
time?
If possible, please help me how to do it.
with thanks
You can always run different instances of a program at the same time. As
you
Hi,
I would suggest you extract the single snapshot from your xtc file and
then run the analysis tool on the single snapshot file.
/Flo
On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote:
Dear All
I use the g_clustersize to examine the cluster decay vs. time during
the
On Sun, 2011-08-28 at 14:21 +0800, Hsin-Lin Chiang wrote:
Hi,
Is part number in extending simulation in ver.4.5.4 cancelled?
Below is my shell script,
#!/bin/bash
a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \
-nt
On Sun, 2011-08-28 at 17:55 +0800, Hsin-Lin Chiang wrote:
Hi Flo,
Thank you for reply.
I got it.
But as you see I also indicate the new names for output files.
Do I get correct result in this kind of situation?
Or I need to rerun it with -noappend
I am not sure, but I assume if you set
On Wed, 2011-08-24 at 12:25 -0400, Juliette N. wrote:
Dear all,
Sorry if my question sounds irrelevant but I am wondering to know if
in gromacs there is any tool for studying properties like sound
wave/acoustic wave (An acoustic wave is a pressure oscillation that
travels through liquid, in
On Thu, 2011-08-18 at 15:44 +0200, Elton Carvalho wrote:
On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu
wrote:
Using g_velacc I can calculate the velocity autocorrelation function of a
group as a vector.
Can I calculate the velocity autocorrelation function as a
]
On Behalf Of Dommert Florian
Sent: 04 August 2011 12:31
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_dipoles - averaging
On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote:
Hello,
Is there any way to output the dipole moment averaged over all molecules
Hello,
I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.
/Flo
On Thu, 2011-07-07 at 09:28 +0200, Ivan
On Wed, 2011-06-01 at 23:37 +0200, Thomas Koller wrote:
Hello,
I calculate the viscosity with g_energy using option -vis (Gromacs
4.0.7):
g_energy -f file.trr -s file.tpr -vis visc.xvg
Why do I get viscosity values only until the half of the simulation
time?
This results from the
On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote:
Hello everybody,
I have a question ragarding the unit of translational and rotational
energy. I am using the gromacs-4.0.7 version and it gives these units
in the ektran.xvg and ekrot.xvg as kJ mol\S-1\N after I used the
command
Hi Andrew,
looking at your protocol, perhaps I can help thermo- and barostating.
This are very important issues as they decide if your final trajectory
samples a canonical phase space that should correspond to the desired
ensemble( Tuckerman and Martyna, J. Phys. Chem. B 2000, 104, 159-178,
Hello Vitaly,
the intention to write out informations to the stdout and the stderr was
that you have the ability to sort it during the analysis. However as
Justin mentionen will write all open pipes into one file.
Cheers,
Flo
On Tue, 2011-05-10 at 13:16 -0400, Vitaly Chaban wrote:
Thanks,
if you haven't changed anything in the ffoplsaa force field files of
gromacs I do not think that you have the correct parametrization. You
wether have to define the short range parameters on the top file or you
change the ffoplsaa files and insert the parameters of Tsuzuki. How how
do this can be
Hello,
oh this nasty ILs ;) I am currently investigating a similar problem,
that deals with PR-coupling and my impression is that Leap-Frog is the
problem and not PR. Currently I am running simulations with md-vv and
MTTK to verify my ideas. On the other hand I am using two tc_groups for
my ILs
On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote:
On 2011-04-18 11.22, Dommert Florian wrote:
Hello,
oh this nasty ILs ;) I am currently investigating a similar problem,
that deals with PR-coupling and my impression is that Leap-Frog is the
problem and not PR. Currently I
On Fri, 2011-04-15 at 15:15 +1000, Mark Abraham wrote:
On 15/04/2011 3:08 PM, bharat gupta wrote:
Reduicng no. of frames means breaking the simulation into smaller
frames ... will it affect the result ??
You can use trjconv -dt to reduce the number of frames per unit time,
not just
Hello,
I have also realized similar behaviour:
NpT simulations performed with a Berendsen barostat give lower densities
than simulations coupled with P-R. However I think this is due to the
fact that I never achieve a pressure of 1bar (it is always around
1.2bar) with P-R even after a previous
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
Hi,
I have a long-chain peptide which has a net charge of +5 . I was
wondering whether the g_dipole will give any reasonable dipole moment
for a molecule with a net charge. Is there any suggestion I should
follow regarding calculation of
On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote:
Dommert Florian skrev 2011-04-01 09.45:
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
Hi,
I have a long-chain peptide which has a net charge of +5 . I was
wondering whether the g_dipole will give any reasonable dipole
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number of sims.
How much long I should run the simulation.
until the average converges.
Nilesh
On Wed, March
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote:
On 2011-03-31 09.25, Dommert Florian wrote:
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number
the simulation for 50ns ans try to save trajectroy of 0.02ps.
Thanks
NIlesh
Nilesh
On Thu, March 31, 2011 5:38 am, Dommert Florian wrote:
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote:
On 2011-03-31 09.25, Dommert Florian wrote:
On Wed, 2011-03-30 at 20:23 +0200, David van
Hello,
g_tcaf gives a reference for the method to calculate \eta. However I can
not find the Palmer JCP 49 (1994), either in a database nor on the JCP
page. As I want to use the method, I first have to get an idea about it
and so I need this article to continue. Has anybody an idea where it is
On Thu, 2011-03-24 at 12:56 +0100, Tsjerk Wassenaar wrote:
Hi Florian,
It should be Phys. Rev. E i.s.o. JCP.
Cheers,
Tsjerk
Thank you very much, I got it.
Cheers,
Flo
--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote:
Hi Nuno,
I have still problems with the insatllation of the 4.0.7 version.
After unpacking of fftw and gromacs, I did:
In the fftw folder:
./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared
--enable-float
On Tue, 2011-03-15 at 05:53 +0100, Thomas Koller wrote:
I have installed Gromacs but if I want to open another terminal and
run another simulation it does not work.
You have to make sure, that the binaries and libraries installed in
$GROMACS/bin and $GROMACS/lib are found by the terminal,
Hello,
it seems FFTW3 is not installed in the LD_LIBRARY_PATH and/or the fftw3
headers can not be found. On Ubuntu, most likely the headers are not
installed (available in the package libfftw3-dev). However it is really
easy to compile FFTW3 yourself and install it inside your $HOME. Then
you do
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