Hi,
start with using as many MPI processes as you have GPUs. GROMACS
will use several OpenMP threads per MPI process to use all your CPU
cores.
You can also do that manually with
mpirun -np 2 mdrun-mpi -ntomp 6
Carsten
On 12/10/2013 10:30 AM, rajat desikan wrote:
Dear all,
I recently
If the system does not explode, everything is correct. Though your
solution is perhaps in the wrong place in relation to the tube.
Dr. Vitaly V. Chaban
On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Justin
Based on your suggestion, I added C-C bond
Dear All.
Hi. I'm want calculation of dimer protein.
My proteins have manganese. But don't have gbsa.itp of manganese.
I'm insert Mn data, but I don't know 'sar, st, pi ...'
What is the values mean?
Thank you.
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Dear ,
I want to bulid a system that the ligand covalently bond with the protein,
could anyone tell how to do this one by one step or give me a tutorial to do
this. thank you very much !
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On Tue, Dec 10, 2013 at 8:11 AM, C.H. Kim poc...@icloud.com wrote:
Dear All.
Hi. I'm want calculation of dimer protein.
My proteins have manganese. But don't have gbsa.itp of manganese.
I'm insert Mn data, but I don't know 'sar, st, pi ...'
What is the values mean?
Please read manual
On Tue, Dec 10, 2013 at 7:54 AM, aixintiankong aixintiank...@126.comwrote:
Dear ,
I want to bulid a system that the ligand covalently bond with the
protein, could anyone tell how to do this one by one step or give me a
tutorial to do this. thank you very much !
On Mon, Dec 9, 2013 at 12:58 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I am calculating the water density inside my membrane protein along Z
directions. I used the a_ri3DC tool in Gridcount which is a patch in
Gromacs for calculation:
a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp
On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi es...@sfu.ca wrote:
Thanks Justin.
I added the bond description in the ffbonded.itp but it does not show in
the topol.top file.
In ffbonded.itp we have:
[ bondtypes ]
; ij func b0 kb
OWHW 10.09572
On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian
atila.petros...@gmail.comwrote:
Dear Justin
Based on your suggestion, I added C-C bond length to z dimension of box
(before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418).
Then I used genion to neutralize system using replacing 2 water molecules
by 2
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I then generated
a .tpr using grompp
When I do any simple gromacs command like:
On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.comwrote:
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I
I have a paracetamol crystal and I would like to estimate the
paracetamol/paracetamol energy of interaction per unitcell.
To do this I am doing the following:
Energy of interaction of paracetamols per unitcell=
Total energy of a unitcell - (Energy of a molecule in the unitcell* number of
the
On Tue, Dec 10, 2013 at 12:31 PM, Shine A shin...@iisertvm.ac.in wrote:
Sir,
I completed a 400 ns MD simulation. But in some part of the trajectory
my protein is just out side the box I selected (triclinic). Is there any
option in gromacs to constrain my protein in box during simulation.
Dear ,
I want to bulid a system that the ligand covalently bond with the protein,
could anyone tell how to do this one by one step or give me a tutorial to do
this. thank you very much !
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* Please search the archive at
On Tue, Dec 10, 2013 at 7:28 PM, aixintiankong aixintiank...@126.comwrote:
Dear ,
I want to bulid a system that the ligand covalently bond with the
protein, could anyone tell how to do this one by one step or give me a
tutorial to do this. thank you very much !
Please refer to the link
Dear Justin,
Thanks for the suggestion.
Producing a .trr in catdcd still failed because it apparently produces a
trajectory without a timestamp. So, I loaded the .dcd into vmd and saved
the coordinates in a .trr file. This worked like a charm :)
Note to self: Install gromacs with the vmd plugin
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