Dear Ravi
Use trjconv -dump ... ( time in ps)
With Best wishes and regards
Rama david.
On Mon, Oct 1, 2012 at 11:15 AM, Ravi Kumar Venkatraman
ravikumarvenkatra...@gmail.com wrote:
Dear All,
How to get a snapshot at a particular time frame from the MDS
run.
Thank
Dear Everyone,
I have two questions about the conversion of binding energy to binding
affinity.
I predicted the binding energy of a protein-membrane complex by umbrella
sampling (based on Justin's tutorial). After sampling, the binding energy
should be the substract of (min-max) PMF. I have
28 sep 2012 kl. 18.53 skrev pauladelgado:
Yes i found this document Computer simulations: Orientation of Lysozyme in
vacuum under the influence of an electric field where i found about the
conditions i mentioned before for vacuum simulations. So what should i do?
Find other literature.
Hi,
Depending on what you aim to do one option might be to make the DNA a pair of
periodic molecules. That would keep them aligned with whatever box vector you
chose. But again, that depends on what you aim to study.
Erik
1 okt 2012 kl. 07.44 skrev 仝督读:
Hi everyone,
I am doing a DNA
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe this error has been discussed before; I have checked previous messages on it but i
could not resolve it. I have done a modified version of the oplsaa forcefield which I
have called ffoplsaamod.n2t. The top file was created successfully.
On 10/1/12 12:43 AM, Ravi Kumar Venkatraman wrote:
Dear All,
To find out gas phase torsional energetics I have restraints
dihedral and calculated the energies. But the Dihedral restraints are not
working properly, its changes +/- 2-5 degree from the specified value. Is
there any
On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Everyone,
I have two questions about the conversion of binding energy to binding
affinity.
I predicted the binding energy of a protein-membrane complex by umbrella
sampling (based on Justin's tutorial). After sampling, the binding energy
On 10/1/12 7:10 AM, Ali Alizadeh wrote:
Dear all users
1- I am trying to simulate a system that contains 1182 methane
molecules(5910 atoms) and 1830 water molecules(5490), I
keep getting these errors.
Something is wrong with the starting configuration, topology, or .mdp settings
(see
On 10/1/12 8:52 AM, venkatesh s wrote:
Respected Gromacs Users,
i am trying to simulate protein peptide
want understand interaction
my protien 210 Amino acid and my peptide only 5 Amino acid, and molecular
types different (between protein peptide )
docked
Thanks for your time and help as always. I will see what I can do about that.
Elie
Date: Mon, 1 Oct 2012 08:38:15 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe this error has
Dear Dudu Tong
Theres a paper on using limited x y z restraints but I have forgotten it. In
any case theres a way to generate 1 2 or 3D positional restraints with just the
grompp , and you can cut and past. The output posre in the help command will
give you a file, and theres a selection for
Hi everybody,
I want to do a md run. But I have a problem. I have additional residues
which are not in the aminoacid.rtp file.
I already read the site about Adding a Residue to a Force Field.
But the problem is that I am not allowed to change anything at the
topology files on the server I want to
On 10/1/12 4:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a md run. But I have a problem. I have additional residues
which are not in the aminoacid.rtp file.
I already read the site about Adding a Residue to a Force Field.
But the problem is that I am
Hi Justin,
thank you very much for the helpful and fast answer :)
On 10/1/12 4:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a md run. But I have a problem. I have additional
residues
which are not in the aminoacid.rtp file.
I already read the
Dear all:
Does anyone know the optimal force field in GROMACS for treating divalent
ions in explicit solvent? Would appreciate any recommendations.
Thanks,
Lili
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I am a bit confused..I am getting different errors though similar in goal. The
error this time is:
Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms
]'Invalid order for directive atomsLet me tell you what I did again: I have
another n2t file ( fftoplsaamod.n2t) which was
Hi Elie,
Your email is a bit confusing but I will try to give you some idea as per my
understanding of your email.
If you want to use top and itp files separately, you should put all the info
(molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and you
should use # include
On Monday 01,October,2012 01:44 PM, 仝督读 wrote:
Hi everyone,
I am doing a DNA simulation in a long simulation box (the lengthen of z is
much larger than x and y). So I want to constrain the DNA molecule lying
along the z axis. But I don't know how to realize this in GROMACS.
Actually I
I have been trying to automate my simulation setup and monitoring. I wrote a
script which calls g_energy, and automatically generates plots of potential
energy from my EM step, temperature from my NVT equilibration step, and
pressure and density from my NPT equilibration step. For each of these
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