Hello,
I need to combine several trajectories (.xtc) and energy file (.edr) pairs.
In the end I need all the conformations of the trajectories and a specific
energy value for each of them.
To combine two trajectories, I use trjcat [1] like this:
trjcat -f first.xtc second.xtc -o combined.xtc
On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Martin Kamp Jensen wrote:
Hello,
I need to combine several trajectories (.xtc) and energy file (.edr)
pairs. In the end I need all the conformations of the trajectories and a
specific energy value for each of them
On Wed, Sep 28, 2011 at 1:33 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote:
On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Martin Kamp Jensen wrote:
Hello,
I need to combine several trajectories (.xtc
On Fri, Jul 15, 2011 at 1:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
**
On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote:
Hello,
I am trying to evaluate energy values of several conformations using a
(pseudo)trajectory. Currently, I am concatenating GROMOS-96 files (.g96) and
using
Hello,
I am trying to evaluate energy values of several conformations using a
(pseudo)trajectory. Currently, I am concatenating GROMOS-96 files (.g96) and
using that as a trajectory. For some reason the second conformation in a
trajectory is ignored. So e.g. if I have three conformations (1.g96,
Hi Mark,
Thanks (again, again) for your input!
On Fri, Nov 12, 2010 at 5:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
Hi,
As far as I understand, a topology (a .top file) and a conformation
(e.g., a .gro file) contain enough
Hi,
As far as I understand, a topology (a .top file) and a conformation (e.g., a
.gro file) contain enough information to calculate the torsion angles of
that specific conformation.
Table 5.5 (page 124) in the GROMACS manual[1] describes possible
interactions (which are contained in the
Hi Mark,
On Sun, Nov 7, 2010 at 2:54 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
Hi Chris,
On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
mitomas...@gmail.com wrote:
Hi,
You need to use md integrator for -rerun to work
Hello,
Hopefully someone can help me understand how to use the mdrun -rerun
functionality, because currently I am confused. I would like to be able to
look up potential energy values for a number of conformations by calling
mdrun -rerun once.
The idea to use mdrun -rerun is from advice given to
/mdrun.html With -rerun an input
trajectory can be given for which forces and energies will be
(re)calculated. Neighbor searching will be performed for every frame, unless
nstlist is zero (see the .mdp file).
Good luck,
Chris
2010/11/6 Martin Kamp Jensen martin.kamp.jen...@gmail.com
Hello
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