[gmx-users] problem of GLUP

[Albert]

Hello:

I've got a protonated GLUP in the protein. I try to run command:

grompp_mpi -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -n

it always claimed 16 atoms doesn't belongs to any 16 atoms are not part 
of any of the T-Coupling groups

I make a new index file by make_ndx like:

 > 1|13

Copied index group 1 'Protein'
Copied index group 13 'GLUP'
Merged two groups with OR: 4960 16 -> 4976

  28 Protein_GLUP        :  4976 atoms


This error is no longer there.

However, I noticed that the speed of my MD simulations become 
unbilevable slow with command in a cluster:

mpirun -np 144 mdrun_mpi -v -s nvt.tpr -c nvt.gro -g nvt.log -x nvt.xtc

  I don't know whether because of this issue. Here is my nvt.mdp settings:


; Temperature coupling parameters
tcoupl          = V-rescale             ; Modified Berendsen thermostat 
using velocity rescaling
tc-grps         = Protein_GLUP POPC  Water_and_ions ; Define groups to 
be coupled separately to temperature bath
tau_t           = 0.1   0.1     0.1     ; Group-wise coupling time 
constant (ps)
ref_t           = 310   310     310     ; Group-wise reference 
temperature (K)

; Centre of mass (COM) motion removal relative to the specified groups
nstcomm         = 1                     ; COM removal frequency (steps)
comm_mode       = Linear                ; Remove COM translation (linear 
/ angular / no)
comm_grps       = Protein_GLUP_POPC_POPG Water_and_ions ; COM removal 
relative to the specified groups
table-extension = 1

I am using 4.6.5 and it was compiled with command:

CMAKE_PREFIX_PATH=/usr/mpi/gcc/openmpi-1.4.3:/home/albert/install/fftw-3.3.3/ 
cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF 
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.5 -DGMX_GPU=OFF 
-DGMX_MPI=ON

thank you very much.

Albert