Hi,
I have used MacroMolecule Builder for similar things.
Erik
On Feb 13, 2013, at 4:41 AM, zugunder wrote:
Hi,
I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some
advice...
I need to simulate a
It shouldn't generate output. It will make your system find your
gromacs installation, however. Try e.g. which mdrun.
Erik
On Feb 13, 2013, at 5:06 AM, David Sáez wrote:
Thanks for your answer Justin. I followed your advice:
When I type
*$ source /usr/local/gromacs/bin/GMXRC*
*$*
Nothing
Dear gromacs users,
I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force
field. Its a dimeric protein with a MG ion and 2 ligands bound to two
active sites. I wish to run the dimer and there would be 4 ligands. I
generated the topology files (.itp) of ligands using SWISSPARAM.
Hello!
I am simulating Aspartate at pH 10, so it needs to be fully deprotonated
(COO-, COO- and NH2).
pdb2gmx allows to easily set side chains to be deprotanted, but is there a
straightforward way to make NH2, not NH3+?
Thank you very much!
Kind regards,
Valentina
Hi Valentina,
Use pdb2gmx -ter
Cheers,
Tsjerk
On Wed, Feb 13, 2013 at 1:22 PM, Valentina Erastova
valentina.erast...@durham.ac.uk wrote:
Hello!
I am simulating Aspartate at pH 10, so it needs to be fully deprotonated
(COO-, COO- and NH2).
pdb2gmx allows to easily set side chains to be
Thank you Tsjerk!
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Aspartate-at-high-pH-tp5005500p5005502.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
Hai,
I need to do simulation of protein at pH 12.I am unable to do
that can you please tell me how to do and how to set up pH conditions.
Thank You.
On Wed, Feb 13, 2013 at 6:08 PM, Valentina
valentina.erast...@durham.ac.ukwrote:
Thank you Tsjerk!
--
On 2/13/13 8:23 AM, Sathish Kumar wrote:
Hai,
I want to do simulation of a protein at pH 12.but I was unable
to do that and I dont know how to set up mdp files for the pH.Can you
please suggest me how to do.
thank You.
This question gets asked
On 2/13/13 5:24 AM, Ansuman Biswas wrote:
Dear gromacs users,
I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force
field. Its a dimeric protein with a MG ion and 2 ligands bound to two
active sites. I wish to run the dimer and there would be 4 ligands. I
generated the
Dear gmx users,
I need to stop my protein jumping inside box. I have used -pbc mol -ur compact
-center command too but still the protein gets moving from one place to other.
Could you please suggest me how to make the protein to stop in one place ?
Moreover, its protein with their ligand.
Hi
Plz try -pbc nojump option...It may work
On Wed, Feb 13, 2013 at 5:29 AM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear gmx users,
I need to stop my protein jumping inside box. I have used -pbc mol -ur
compact -center command too but still the protein gets moving from one
place to other.
On 2/13/13 8:47 AM, Naga Sundar wrote:
Hi
Plz try -pbc nojump option...It may work
Several iterations of trjconv are often needed to achieve the desired
representation. Indeed, the first step to removing jumps should be -pbc
nojump...which removes jumps ;)
-Justin
On Wed, Feb
Hi,
With tau_t=2 the sd1 integrator should be ok.
But in 4.6.1, which will be released this week, the performance issues with the
sd integrator are fixed.
Cheers,
Berk
Date: Wed, 13 Feb 2013 09:19:46 +0300
From: jmsstarli...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] on the
Dear gromacs users,
I would like to compute the transition time gauche-trans for dihedral angles.
For that, I used this command :
g_angle_mpi -f myfile.xtc -n dihedral.ndx -b 25000 -e 3 -type dihedral
-chandler -avercorr -oc myoutput.xvg
I have dihedral autocorrelation function C(t) but I
Hello all,
Does somebody know where i can find the latest GROMOS force field (i.e.
GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ?
[1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247−1264 doi:
http://pubs.acs.org/doi/citedby/10.1021/ct300156h
Thank you
Stephane--
On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/12/13 9:40 AM, Steven Neumann wrote:
Dear Gmx Users,
I know it is possible to combine windows
Dear Steven,
There is no universal method to do this and many people spend years
studying the various techniques. However,
http://pubs.acs.org/doi/abs/10.1021/ct900369w gives an overview of some of
the most widespread techniques used and its references will provide
further details. Futhermore,
I have tried the -pbc nojump options too, but still the protein goes from
center place to corner of the box within 4 ns. Actually it a myoglobin protein
which has heme and ligand atom together.
- orig.Message -
From : gmx-users-requ...@gromacs.org
To :
Message: 8
Date: Wed, 13 Feb 2013 08:28:00 -0500
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] md with multiple ligands
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 511b94e0.4040...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1;
Dear gmx,
I've used -pbc nojump options but still the protein goes all around the box
within 4ns. Any specific command to avoid this ? It's a myoglobin protein!
- orig.Message -
From : gmx-users-requ...@gromacs.org
To : gmx-users@gromacs.org
Sent date :
Hi, dear developers!
I want to ask you abou dynamics in implicit solvent. I have a complex of
animal protein - dimer/trimer. After modeling by homology I have built
another one from the plant organism. Dimer/trimer was constructed with
superposition method. The question is - can I use imlicit
Dear Gromacs Forum,
I want to do RNA simulation using Gromacs. I have installed gromacs 4.5.5
and i found Charmm force field present in it. Can I use this force field for
my simulation. I am asking this because I heard that Charmm force field in
Gromacs is incomplete and different from the one
Original Message
Subject: Re: gmx-users Digest, Vol 106, Issue 68
From:ansuman@localhost
Date:Thu, February 14, 2013 10:16 am
To: gmx-users@gromacs.org
--
hi all,
i have done scattering function analysis using g_rdf command for
polymer-solvent system. i got the plot of scattering vector q(1/nm) vs
intensity .now i want to convert the scattering vector (q) value in to
distance i.e. 'd' the fundamental polymer books have the relation for light
Dear Gromacs Users!
I have completed 100ns md trajectory.
I 'd like to go on that simulation adding extra 100 ns to the existing
trajectory (with appending of both trajectories in single file during
that simulation)
If I do it just via
mdrun -v -cpi md -deffnm md
the simulation have not gone
On 2013-02-14 07:02, fayaz wrote:
Dear Gromacs Forum,
I want to do RNA simulation using Gromacs. I have installed gromacs 4.5.5
and i found Charmm force field present in it. Can I use this force field for
my simulation. I am asking this because I heard that Charmm force field in
Gromacs is
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