[gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

anu chandra anu80125 at gmail.com
Wed Aug 19 13:22:24 CEST 2015

Dear Gromacs users,

I just noticed that during simulation 'mdrun'  writes gro file in two
formats - one with broken molecules at the boundaries and other one where
surface molecules are perfectly wrapped. Interestingly, this difference in
format depends on where I run the simulation - either in a cluster or in my
local 8-core desktop machine. Using 'mdrun' in cluster gives gro file with
broken molecules at the boundaries and my  desktop workstation gives the
one with complete molecules at the surface. Below is the mdp file I used
for simulation in both case


define                  = -DPOSRES_MD
integrator              = md
dt                      = 0.002
nsteps                  = 50000
nstlog                  = 1000
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 1000
nstcalcenergy           = 100
nstenergy               = 1000
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
pbc                     = xyz
tcoupl                  = Nose-Hoover
tc_grps                 = Protein POPC CL_SOL
tau_t                   = 0.5    0.5     0.5
ref_t                   = 305.0    305.0    305.0
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 4.5e-5   4.5e-5
ref_p                   = 1.0     1.0
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC CL_SOL
refcoord_scaling        = com

May I know what is making this difference? Due to the presence of broken
molecules, I failed to visualizing the trajectories (.trr file) using VMD.
Though I could make a gro file with complete molecules at the boundaries
using  trjconv command,

*trjconv -f input.gro -o ouput.gro -s input.tpr -pbc mol*
the visualization of trr file with output.gro also shows long bond between
atoms across the boundaries.  Please help me to rectify this issue with
visualizing the trr file.

In server, following grommp and mdrun commands are used,

*gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
index.ndx -p topol.topmpirun -ppn 16 -np 64 gmx_mpi mdrun -deffnm MD5*

and, in my desktop workstation following commands are used

*gmx grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
index.ndx -p topol.topgmx mdrun -nt 8 -deffnm MD5*

Many thanks


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