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 n
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 $GROMACS/lib are found by the terminal,
On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote:
> Hi Nuno,
>
> I have still problems with the insatllation of the 4.0.7 version.
>
> After unpacking of fftw and gromacs, I did:
>
> In the fftw folder:
>
> ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared
> --enable-f
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
and
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
Pfaffenwaldr
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 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 tak
t;
> I will run 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 20
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
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 t
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 eq
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 jus
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 du
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
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 f
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,
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,
DOI:10
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
> co
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 f
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 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,
opic
> tau_p = 2.0
> ref_p = 1.0
> compressibility = 4.5e-5
>
>
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp= 300.0
> gen_seed= -1
>
>
>
> On Fri, Feb 24, 2012
or a certain dihedral they are even set
to zero. 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
>
sired accuracy.
Hence you can check if the positive Coulomb term is an artefact of low
accuracy.
/Flo
> On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian
> wrote:
> On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote:
> > The ionic liquid is bistriflate N-methyl-N
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_
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 wit
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 molecu
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
> > Subject: Re: [gmx-users] g_msd with input by trjconv -pbc nojump:a
> > concern
> > To: Discussion li
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
authors
ly, there
parameters of for example 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
> >> Hi Florian,
> >> >
> >> > I believe the ion parameters are the Aaqvist parameters:
> >> > ie
> >> > http://pubs.acs.org/doi/abs/10.1021/j100384a009
> >> >
> >> > Cheers
> >> >
> >> >
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 b
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
> >
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
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 pa
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
> > parameter
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 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?
>
>
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
On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote:
> Hello,
>
> 2012/5/3 Dommert Florian
> On Thu, 2012-05-03 at 07:32 +0200, Albert wrote:
> > hello:
> >
> > I wondering are the three thermostat methods: Langevin,
>
On Thu, 2012-05-03 at 11:31 +0200, francesco oteri wrote:
>
>
> 2012/5/3 Dommert Florian
> On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote:
> > Hello,
> >
> > 2012/5/3 Dommert Florian
> > On Thu, 201
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,
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
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 wrote:
> > salam,
> > man mishnasametun?
> > mozoe naghas
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 ca
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, "c
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 th
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 p
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 probl
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 Len
A
and
http://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
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 pr
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 distri
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 a
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 essentia
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
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 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
> line
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 Gladic
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 or
> for each molecule separately (and not the total dipole moment of the
> simulation box) ?
>
Yes, the tool g_current decomposes the total dipole m
300.00 K
> and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911
> Too less points for a fit.
>
> I am not sure, where to find the dipole moment for each of the four molecules.
>
> Many thanks
> Andreas
>
>
> > -Original Message-
> >
On Thu, 2011-08-18 at 15:44 +0200, Elton Carvalho wrote:
> On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal
> 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 scalar?
>
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 liqui
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
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 y
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 ag
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.
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
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 ne
Forwarded Message
From: Sanku M
Reply-to: Sanku M
To: Dommert Florian
Subject: Re: [gmx-users] BD with Hydrodynamic interactions?
Date: Mon, 26 Sep 2011 04:07:38 -0700 (PDT)
> I did not mean lattice boltzmann by BD. > By BD I meant Brownian
Dynamics. In general, for ac
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