On 3/05/2010 7:55 AM, Florian Dommert wrote:
On 30.04.2010, at 16:04, Esztermann, Ansgar wrote:
On Apr 30, 2010, at 14:46 , Rohit Farmer wrote:
Hi everyone..
I just made a small two node condor cluster and was trying to run gromacs on it
... so i used the vanilla environment and placed
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Hello everyone,
I have two protein structures, and the insides of both are not exposed to
water.
One structure contains two oppositely charges residues (GLU and LYS) facing
each other. The second structure contains a GLU residue only.
Upon minimization I had expected the coloumb energies of
abdullah ahmed wrote:
Hello everyone,
I have two protein structures, and the insides of both are not exposed
to water.
One structure contains two oppositely charges residues (GLU and LYS)
facing each other. The second structure contains a GLU residue only.
Upon minimization I had expected
Thank you for your reply,
However, I can not use MD.
I would simply like to ask whether I am correct in assuming that the minimized
energies of the two structures should be very different.
Date: Tue, 4 May 2010 08:41:15 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re:
abdullah ahmed wrote:
Thank you for your reply,
However, I can not use MD.
I would simply like to ask whether I am correct in assuming that the
minimized energies of the two structures should be very different.
What exactly are you measuring? The Coulombic energy of the system? If so,
The charged residues are on the inside of the structure, and so are not
affected by the solvent. There are also no other charged residues in the
structure. Furthermore, the structure is quite small 22 (residues). So I am
still tempted to say that the coloumbic energy of the system should be
Do single-point MM/PBSA calculations. That's an energy value. But they may or
may not be accurate. Energy values as you put them are not simple and you may
need to run a simulation in order to obtain a proper ensemble. Such a
simulation is not for refining the structure, it's to obtain an
abdullah ahmed wrote:
The charged residues are on the inside of the structure, and so are not
affected by the solvent. There are also no other charged residues in the
structure. Furthermore, the structure is quite small 22 (residues). So I
am still tempted to say that the coloumbic energy of
On 5/05/2010 12:27 AM, abdullah ahmed wrote:
The charged residues are on the inside of the structure, and so are not
affected by the solvent. There are also no other charged residues in the
structure. Furthermore, the structure is quite small 22 (residues). So I
am still tempted to say that the
Dear all,
I have simulated a small peptide (+2 charge at pH=7) in water. Then i
calculate the interaction energy using energy_grps = Protein
SOL. The value of different energy terms are as
follows:
Hi Vijaya,
please check out the newest 4.0 version from the git release-4-0-patches
branch. The make_edi problem should be fixed there.
Regards,
Carsten
On Apr 26, 2010, at 11:19 PM, vijaya subramanian wrote:
Hi
I checked again with Gromacs 4.0.7 and I find that I have a problem
with
Hi !
I am a newby on gromacs. Ive run dynamics of an ATP binding domain without
ligand, but now, as the crystal structure with the bound ADP is published, I
would like to see its dynamics. However as I started, I realized that
topologies of ADP and ATP are not present in OPLS .itp file. Did
Hi,
I am trying to construct a PMF profile for a phosphate ion passing
through a membrane protein using umbrella sampling with GROMACS 4.0.5.
I have performed the umbrella sampling simulations using the following
mdp options and I am now attempting to construct the PMF using g_wham.
; Pull
Dear all
I would like to draw your attention to this Summer School on GPU programming.
The Summer School in e-Science with Many-Core CPU/GPU Processors is
planned for the 3rd week of June in Braga, Portugal, and is the first
course in Europe given by two NVIDIA senior members and a Professor
I have been working through some sample problems and now I am at the stage
where I need to settle on a consistent setup for simulation of short peptides
in aqueous solution. I've been through the documentation repeatedly, but there
are a couple things on which I am unclear.
1) I am
Hi Carsten
A couple of quick questions:
I already have gromacs-4.0.7 downloaded from the gromacs website. I found that
I couldn't
use git checkout --track -b release-4-0-patches origin/release-4-0-patches to
get the patches.
fatal: Not a git repository
Do I have to uninstall gromacs-4.0.7
On 5/05/2010 6:56 AM, vijaya subramanian wrote:
Hi Carsten
A couple of quick questions:
I already have gromacs-4.0.7 downloaded from the gromacs website. I
found that I couldn't
use git checkout --track -b release-4-0-patches
origin/release-4-0-patches to get the patches.
fatal: Not a git
Hi ALL,
How can I obtain the residence time of each hydrogen bond during a
simulation? I think the -hbn and -hbm options of g_hbond has to be used, but
how? Is there any script to extract that data? And what is the difference
between the residence time and the life time of a hydrogen bond? Any
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