Hi gmx-users,
I need to generate a FCC unit cell (in fact a face centered cubic lattice)
in order to produce a nanocristal. I would like to know if is possible
to make this using directly GROMACS. In affirmative case, as I can make it?
Thanks in advance
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Eudes Fileti wrote:
Hi gmx-users,
I need to generate a FCC unit cell (in fact a face centered cubic lattice)
in order to produce a nanocristal. I would like to know if is possible
to make this using directly GROMACS. In affirmative case, as I can make it?
Thanks in advance
Andrea C. Vaiana wrote:
Hello everyone,
I'm trying to find a better way of demuxing REMD runs, I wrote a python
script to do this but it is very slow because it relies on system calls
to trjconv in order to read/write frames. I checked the documentation
and mailing lists, it seems that this
Hello,
Instead of using system calls, you may also use the pymacs python
interface by Daniel Seelinger:
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/dseelig/pymacs.html
You can access all information in an xtc file in an object-oriented manner.
Nikos
Andrea C. Vaiana wrote:
Hello
Dear All,
I am using Gromacs 3.1.1 with the AMBER port. After following the
instructions on the ffamber web-page, pdb2gmx works fine. But according
to point 6:
... However, for nucleic acids this also often causes pdb2gmx to
replace an H atom in the first residue of all nucleic acid chains
Dear GROMACS users,
Here I have implemented the k-means clustering algorithm in the
original GROMACS module, gmx_cluster.c (called by the wrapper g_cluster).
k-means is a heuristic algorithm that finds the partition of n points
(conformations) in k groups (clusters), such that the sum of the
Thank you very much for your answer!
I have check manual in chapter4. I am still confused about this sentence.
As we know, each dihedral was counted only once(?) in the program. however,
if several torsional dihedral angles with different parameters can be defined
on the same set of atoms i, j, k,
Dear all,
I am working on a tripeptide and would like to calculate Potential
Mean Force for the tripeptide. Suggestions to calculate PMF are
awaited.
Regards,
Chetana
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gmx-users mailing listgmx-users@gromacs.org
Thank you very much for your answer!
I have check manual in chapter4. I am still confused about this sentence.
Which sentence? Please either quote it, or refer precisely to it with a
reference. Nobody is going to read the whole of chapter 4 to find the one
relevant sentence that is confusing
Dear all,
I am working on a tripeptide and would like to calculate Potential
Mean Force for the tripeptide. Suggestions to calculate PMF are
awaited.
How about looking for PMF in the manual and reading what it has to say there?
Mark
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gmx-users
Hello All.
I am simulating t4 lysozyme with NAG. I have added a short peptide label
to lysozyme which binds calcium ions.
During the simulation there is some drift. I am attempting to re-center
the protein+label+NAG+Ca ion.
I am using trjconv and have setup an index file that contains only
Nikos Sgourakis wrote:
Dear GROMACS users,
Here I have implemented the k-means clustering algorithm in the original
GROMACS module, gmx_cluster.c (called by the wrapper g_cluster).
k-means is a heuristic algorithm that finds the partition of n points
(conformations) in k groups (clusters),
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