Dear,
i want to get a representative frame from a trajectory to analyze the
interaction between the protein and ligand. first i use the g_rms command to
get the rmsd-matrix.xpm file from 80ns to 100ns. The min rmsd is 0 and the max
is 6. The next step i will use the g_culster to get the rep
Dear,
i want to get a representative frame from a trajectory to analyze the
interaction between the protein and ligand. first i use the g_rms command to
get the rmsd-matrix.xpm file from 80ns to 100ns. The min rmsd is 0 and the max
is 6. The next step i will use the g_culster to get the rep
hi my friends, please help me
i use following command for install gromacs:
CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake ..
-DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON
-DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gr
You seem to be missing a -D infront of the thread mpi option.
On 29 Nov 2013 16:54, Mahboobeh Eslami wrote:
hi my friends, please help me
i use following command for install gromacs:
CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake ..
-DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUIL
Thank you for your help
What command do I use to use 8 cores
Good luck
On Friday, November 29, 2013 7:22 PM, Mahboobeh Eslami
wrote:
hi my friends, please help me
i use following command for install gromacs:
CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake ..
-DGMX
i want to install gromacs4.6.3 on 8 core.
i use following command:
CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake ..
-DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON
-DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs
i
As far as I understand, if you have configured it correctly with that version,
it will use all available cores unless you specify otherwise. The precise
command for this escapes me for the moment but it is documented on the gromacs
website. When you run mdrun it will tell you how many threads it
You don't; you configure your MPI environment to have 8 ranks, which could
be as simple as mpirun -np 8 mdrun_mpi.
Generally you do not need double precision with GROMACS, unless you can say
exactly why you need to trade away your simulation performance.
Mark
On Nov 29, 2013 9:15 PM, "Mahboobeh E
pdb2gmx produces error message:
Fatal error:
Residue 'E' not found in residue topology database
But there is no "Residue 'E' " in my pdb file (see below). I have verified
that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx
does identify the ACE and NME caps.
COMPNDUNNA
On 11/29/13 7:23 PM, kolnkempff wrote:
pdb2gmx produces error message:
Fatal error:
Residue 'E' not found in residue topology database
But there is no "Residue 'E' " in my pdb file (see below). I have verified
that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx
does iden
The fluctuation is often of the order of magnitude of itself.
It's that matters.
On Thu, Nov 28, 2013 at 1:26 PM, bipin singh wrote:
> Thanks for you reply Prof. Shirts.
>
> I have plotted the dh/dl values (link mentioned below), but I am not sure
> whether the fluctuation is in acceptable ra
Thank you Prof. Shirts for your help and suggestions.
On Sat, Nov 30, 2013 at 6:04 AM, Michael Shirts wrote:
> The fluctuation is often of the order of magnitude of itself.
> It's that matters.
>
>
>
> On Thu, Nov 28, 2013 at 1:26 PM, bipin singh wrote:
> > Thanks for you reply Prof. Shirts.
Dear users
is there any way to retrieve box size and othe properties from .trr or .tpr
file?
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