Hi there, I'm installing gromacs with these series of commands,
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install cmake
cmake --version
sudo apt-get install build-essential
pwd
cd Downloads/
wget http://gerrit.gromacs.org/download/regressiontests-5.1.1.tar.gz
tar xvzf regressio
Dear all,
Does there exist any differences between the steps to follow for protein
and protein-protein complex md simulation?
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*Shyantani Maiti*
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Hi, Can anyone tell me the steps and commands for performing multiple runs of
50 ns for same protein-ligand system? Also the clustering for further analyses.
Thanks.
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Can molecular dynamic simulation be performed over protein-protein
complexes using gromacs?
Thanking you,
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*Shyantani Maiti*
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Hi,
Try getting a more up to date version from
http://manual.gromacs.org/documentation/ and follow the quick installation
guide there.
Mark
On Sat, Feb 24, 2018, 10:25 banijamali_fs wrote:
> Hi there, I'm installing gromacs with these series of commands,
>
> sudo apt-get update
>
> sudo apt-ge
Hi,
Following the Lusozume tutorial, I face an error at the step of generating
ions.tpr which says too many warnings.
$ gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the
Dear Cheng,
Gromacs is open source. Implement this at your own will. If there is a
sufficient interest in such a feature it might even have a place in the
official release at some point.
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie
Dear Shayantani,
The output you quote show a negative potential energy. Is that not for the run
you refer to?
(With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.)
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Cur
Hi,
Updating my post. The problem has been observed in two different machine
systems (the latest I have found the problem was the skylake nodes in
tacc). I assumed it has to be some communication bug of coordinates and
forces in the pull part of the code. Probably observed in my case
because o
Hi,
My (thoroughly uneducated) guess is that the spikes are related to the pull
distance approaching half of the dimensions of the cell. Not all flavours
of pulling can handle this. Might that be the issue?
Mark
On Sat, Feb 24, 2018, 17:55 alfredo wrote:
> Hi,
> Updating my post. The problem
Hi Mark,
Thanks for your comment. No, that is not the problem. At that location
the center of mass of the peptide is deep inside the membrane,
separation between the two pulling groups is 0.4 nm and the dimension of
the cell along z is more than 10 nm. I am only pulling along the z
direction.
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