Hello users,
I was going through a literature ( dx.doi.org/10.1021/ct300342n ). Here
they use GROMACS 4.5 version and use SETTLE constraint for bonds in water
I wanted to know how can I apply SETTLE method in GROMACS 5.1.2.
Regards,
Amit Behera
--
Gromacs Users mailing list
* Please search the a
Hi,
The water .itp files distributed with GROMACS are all set up to use SETTLE
by default, e.g. via the [ settles ] directive.
Mark
On Mon, Jul 4, 2016 at 10:49 AM wrote:
> Hello users,
> I was going through a literature ( dx.doi.org/10.1021/ct300342n ). Here
> they use GROMACS 4.5 version and
Dear GMX usere
my problems is in the assigning the ligand charges in protein-ligand
simulation
(for instance :acetaminophen )
i acquired (*.itp ) file by PRODRG (after optimization by gaussian
software) and ATB server as below.
which one is appropriate to my MD simulation by gromaces:
*atom*
Dear Mark,
Thank you very much for your help.
I checked the .itp file of my new parametrized molecule (THF) generated by
pdb2gmx and it is not completed (only [atoms] entry, there is no [bonds],
[angles] or [dihedrals] entries. Effectively, pdb2gmx failed to generate the
topology of the THF.
Hi Justin,
Thank you very much for your answer. I figured out that I did not save velocity
during my simulation. Now it's ok.
Best,
Tai
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of J
Dear gmx users,
I'm working on a Hemprotein (homodimer) and I'm having some troubles with
pdb2gmx in order to recognize the Fe-S bond (between the hem and a residue of
my protein):
In my pdb2gmx command, I'm using chainsep option in a way that the HEM and the
protein belongs to the same chai
Hi all!
The potential for the angle-vibration potential in CHARMM is V = k(a - a0)^2.
Its corresponding force field is proportional to 1/sin(a) which blows up when a
approaches \pi or when the molecule is in linear arrangement. I am wondering
how Gromacs calculates the angle-bending potential o
On 7/4/16 5:43 AM, zeineb SI CHAIB wrote:
Dear Mark,
Thank you very much for your help.
I checked the .itp file of my new parametrized molecule (THF) generated by
pdb2gmx and it is not completed (only [atoms] entry, there is no [bonds],
[angles] or [dihedrals] entries. Effectively, pdb2gmx
On 7/4/16 5:19 AM, elham tazikeh wrote:
Dear GMX usere
my problems is in the assigning the ligand charges in protein-ligand
simulation
(for instance :acetaminophen )
i acquired (*.itp ) file by PRODRG (after optimization by gaussian
software) and ATB server as below.
which one is appropriat
Thank you very much Justin,
I'll add the [bonds] parameters and I'll let you know.
Regards.
Zeineb
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't p
Hi,
You can also look at the THF rtp entries for the gromos forcefields, as
rough guides.
Matk
On Mon, 4 Jul 2016 13:30 zeineb SI CHAIB wrote:
> Thank you very much Justin,
>
> I'll add the [bonds] parameters and I'll let you know.
>
> Regards.
>
> Zeineb
>
>
> --
> Gromacs Users mailing list
hello
i try to install gromacs in my laptop with this cpu :AMD Dual-core
processor E-350 and Linux operating system ubuntu 14.04
i installed gromacs-5.1.2 and gromacs-5 but both of these versions get
error about grompp .and installation from software center (gromacs-4.5.6)
get this error: illegal
Dear GMX users,
the last week I began using a GPU cluster and I am now getting an error I have
never seen before:
85 Source code file:
/homea/hmu24/hmu240/Codes/gromacs/src/gromacs/utility/smalloc.c, line: 227
86
87 Fatal error:
88 Not enough memory. Failed to realloc 323880 bytes for sort
Hi,
Hmm that's a new one on me, too! How many particles has this system? Can
you please open an issue at
https://redmine.gromacs.org/projects/gromacs/issues/new and attach your
.tpr?
Mark
On Mon, Jul 4, 2016 at 2:16 PM Carlo Camilloni
wrote:
> Dear GMX users,
>
> the last week I began using a
Hi,
You need to teach your shell which version of GROMACS you want to use, or
it will do what it can from the existing environment. For example,
http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#getting-access-to-gromacs-after-installation
Mark
On Mon, Jul 4, 2016 at 2:05 PM
On 04/07/16 12:11, Mr Bernard Ramos wrote:
Hi all!
The potential for the angle-vibration potential in CHARMM is V = k(a - a0)^2.
Its corresponding force field is proportional to 1/sin(a) which blows up when a
approaches \pi or when the molecule is in linear arrangement. I am wondering
how Gro
Dear gromacs user,
I was wondering if anybody has any experience with binding free energy
calculation of a molecule (here amino acid) into a solid surface in aqueous
solution using alchemical analysis?
I have already tried successfully the tutorial of methane solvation free
energy in water and so
Dear Justin,
my C++ code is correct, but diffusion constant of my code and Gromacs are
not same.
Perhaps coordinates make this problem.
coordinates of atoms in the different frames gathered by "g_traj". Is this
true? Some of the coordinates are out of the box! negative or larger than
box size.
Th
Hi Alex,
if you use an alchemical method, your answer will be a complex mixture of
solvation and adsorption free energy, since the molecule may diffuse
freely, so it might be closer or farther from the surface depending on your
initial setup, simulation parameters, length of the simulation and so
On 04/07/16 16:20, pari lotfi wrote:
Dear Justin,
my C++ code is correct, but diffusion constant of my code and Gromacs are
not same.
Perhaps coordinates make this problem.
coordinates of atoms in the different frames gathered by "g_traj". Is this
true? Some of the coordinates are out of the box
Hi David!
Thanks for the reply. I may need to check the details myself. Where in the
Gromacs manual can I find them? Are there references I can check. I am only
interested in knowing that the force field does not blow up. It would be a
relief to know it does not diverege. Thanks
Bernard
Should I remove gromacs that I've installed?
i don't understand what this means : source
/your/installation/prefix/here/bin/GMXRC
On Mon, Jul 4, 2016 at 5:03 PM, Mark Abraham
wrote:
> Hi,
>
> You need to teach your shell which version of GROMACS you want to use, or
> it will do what it can from
Hi,
On Mon, Jul 4, 2016 at 6:36 PM roshanak starlight
wrote:
> Should I remove gromacs that I've installed?
>
Depends which one you want to use. If you don't know, you want 5.1.2.
> i don't understand what this means : source
> /your/installation/prefix/here/bin/GMXRC
>
GROMACS got installed
when i was installing , i typed this: 'source
/usr/local/gromacs/bin/GMXRC' after 'sudo make install' command . and then
gmx grompp -h .and i can see GMXRC in this adress in my laptop.is
everything right?
but why dose not know gmx and it get this massage that program grompp is
currently not instal
but my folder which contains downloaded gromacs-5.1 and cmake and fftw are
within other address
On Mon, Jul 4, 2016 at 11:32 PM, roshanak starlight wrote:
> when i was installing , i typed this: 'source
> /usr/local/gromacs/bin/GMXRC' after 'sudo make install' command . and then
> gmx grompp -
You would want to perturb your amino acid in both the free (unbound) and
complex (bound) aqueous states.
Then if you subtract the free energy change from perturbing the free
ligand, from that of perturbing the bound ligand, you should close the
non-physical thermodynamic cycle and get a binding fr
Just to clarify, the formula should be:
dG (bind) = dG (complex) - dG (solv)
Billy
On Tuesday, 5 July 2016, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:
> You would want to perturb your amino acid in both the free (unbound) and
> complex (bound) aqueous states.
>
> Then
Dear All,
In my MD simulation I only added counter ions (20 Na+ ions) to neutralize
the system. Now I want to do MM_PBSA calculations for my MD runs. In order
to do perform polar solvation energy, I have to define parameters pcon and
ncon.
According to my system what values should be assigned to t
Post this on g_mmpbsa forum https://groups.google.com/forum/#!forum/g_mmpbsa
Regards
Sarath
On 5 July 2016 at 08:57, Amali Guruge wrote:
> Dear All,
>
> In my MD simulation I only added counter ions (20 Na+ ions) to neutralize
> the system. Now I want to do MM_PBSA calculations for my MD runs.
Dear users,
I have centos 6.6 server with 64 processors. I want to do parallel
simulations by enabling the MPI threads. For installation of gromacs can I
follow the typical gromacs installation guide which is available in the
installation instructions?
Thanks in advance
Surya
Graduate student
Ind
30 matches
Mail list logo
