Fellow users,I have read several emails exchanged in this discussion list where g_dist is presented as a better choice for observing salt bridges in the trajectory. And I'm totally inclined to agree with that, but that would be the case where you already know which are the SBs present in the
Fellow users,
I have read several emails exchanged in this discussion list where
g_dist is presented as a better choice for observing salt bridges in the
trajectory. And I'm totally inclined to agree with that, but that would
be the case where you already know which are the SBs present in the
open your .mdp in an editor and under energygrps, add " ProteinSurface" after the last term.Run grompp using this .mdp and create a new .tpr. Then use the command line Justin mentioned
open your .mdp in an editor and under energygrps, add ProteinSurface
after the last term.
Run grompp using this .mdp and create a new .tpr. Then use the command
line Justin mentioned last.
Diogo
That can certainly work for me! Especially because I know my groups
functional groups. I guess if one was still in doubt what to focus on,
then my idea could still be useful (with a bit more of work).
Now, just so I get things right:
1. I got to make ONE group in my .ndx that contains all my
At the end of your topology file, what molecules do you have written
down?
You should have something like:
Protein
Surface
SOL
Ion (if you needed to equilibrate system)
Diogo
--
Date: Thu,
I've been reading many tentatives of breaking down the long range term
of interaction, but have not found a feedback if any actually worked. Is
there a working method of achieving this?
Att.
Diogo
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Hi all,
I have two proteins which I've docked and obtained two models, dock1 and
dock2. Both corroborate, to some point, with literature experiments.
I ran both models in a 76ns simulation, using 43a1 force field and PME.
I have managed to map all salt bridges and their distances through the
, Diogo Martins de Sá wrote:
Hi all,
I have two proteins which I've docked and obtained two models, dock1 and
dock2. Both corroborate, to some point, with literature experiments.
I ran both models in a 76ns simulation, using 43a1 force field and PME.
I have managed to map all salt bridges
Hi guys,
Can any one show a picture of how a normal enemat output should look
like?
Since the bug in enemat was only fixed in version 4.6.5, I have a very
basic question:
Can I install a newer version of gromac (say 5) and use its enemat to
treat .edr files from older versions (i.e. 4.5.3 and
Hi all,
I have two proteins which I've docked and obtained two models, dock1 and
dock2. Both corroborate, to some point, with literature experiments.
I ran both models in a 76ns simulation, using 43a1 force field and PME.
I have managed to map all salt bridges and their distances through the
Hello guys,
I'd like to do make an energy matrix of every aminoacid of a simulation
of two interacting proteins. I know enemat can assess the matrix, but
for this I have to define energygroups in .mdp files. What would be the
easiest way to achieve this?
Thanks in advance.
Regards,
Diogo
--
Hello guys,
I'd like to do make an energy matrix of every aminoacid of a simulation
of two interacting proteins. I know enemat can assess the matrix, but
for this I have to define energygroups in .mdp files. What would be the
easiest way to achieve this?
I guess if I am going to find an easier
Hi Nikhil, You can get CUDA toolkit 7.5 using apt-get install nvidia-cuda-dev nvidia-cuda-toolkit. Also, if you open the link I've sent, you`ll see the step on how to install directly from provider. NAMD ran with CUDA this way. So it is supported. Installing directly with apt-get gives the same
Hi Florent, you''ve read my mind! I've just tried that using gcc-4.8 and g++-4.8. the "cmake" step worked like before but "make" gave the exact same error. Does anyone know what the "Building NVCC" does? NVCC is the nvidia cuda compiler, maybe it was not found? I found this: CUDA codes runs on
Hi Mark and Szilard, Thanks for all the help. Just to make sure I understood, I should run cmake like this: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda-7.5 -DCMAKE_C_FLAGS="-D_FORCE_INLINES" or should I try to modify a
Hi Mark, I know, but at that moment I wasn't working in the same room as the CPU and I wanted to be sure on what I had to try next. I tried the cmake command and got the same message. I used grep -R -I "CUDA_NVCC_FLAGS" and grep -R -I "CMAKE_CXX_FLAGS" to find what files I could try to add
Hi Mark, I know, but at that moment I wasn't working in the same room as the CPU and I wanted to be sure on what I had to try next. I tried the cmake command and got the same message. I used grep -R -I "CUDA_NVCC_FLAGS" and grep -R -I "CMAKE_CXX_FLAGS" to find what files I could try to add
Hi guys, I am running kubuntu 16.04 and installed CUDA toolkit 7.5 like was done here: https://www.pugetsystems.com/labs/articles/NVIDIA-CUDA-with-Ubuntu-16-04-beta-on-a-laptop-if-you-just-cannot-wait-775/ I used cmake with the following command line: cmake .. -DGMX_BUILD_OWN_FFTW=ON
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