[gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)

[Andrea Minoia]

Mark,
thank you for the fast reply. My original mdp, the one I used to run the
dynamics is

nstcgsteep               = 1000
nbfgscorr                = 10
emstep                   = 0.02
emtol                    = 10
dt                       = 0.002
nsteps                   = 15000000
comm-mode                = none
nstcomm                  = 1
comm_grps                = system
nstxout                  = 1000
nstvout                  = 1000
nstfout                  =
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 1000
xtc_grps                 = system
energygrps               = CNT pcl
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.5
coulombtype              = cut-off
rcoulomb                 = 1.5
vdwtype                  = cut-off
rvdw                     = 1.5
periodic_molecules       = yes
tcoupl                   = nose-hoover
tc-grps                  = system
tau_t                    = 0.5
ref_t                    = 300
Pcoupl                   = no
pcoupltype               = isotropic
tau_p                    = 5.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = no
gen_temp                 = 300
gen_seed                 = -1
constraints              = all-bonds
constraint_algorithm     = LINCS
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30
freezegrps               = CNT
freezedim                = Y Y Y
nwall                    = 0
wall_type                = 9-3
wall_r_linpot            = -1
wall_atomtype            =
wall_density             =
wall_ewald_zfac          = 3
ewald_geometry           = 3d
energygrp_excl           = CNT CNT

with this I have created, of course the tpr used to run the dynamic:
runmd.tpr. With make_ndx, I have an index file containing only the pcl
group. using this index file, i have created the new tpr, rerun.tpr,  from
the original runmd.tpr file using tpbconv.
as far as I see, the only exclusion is for the CNT CNT groups (last line of
the mdp file above).

a gmxdump of rerun.tpr gives me this info about groups (at the end of the
file)

Group statistics
T-Coupling  :     756  (total 756 atoms)
Energy Mon. :     756      0      0  (total 756 atoms)
Acceleration:     756  (total 756 atoms)
Freeze      :     756      0  (total 756 atoms)
User1       :     756  (total 756 atoms)
User2       :     756  (total 756 atoms)
VCM         :     756  (total 756 atoms)
XTC         :     756  (total 756 atoms)
Or. Res. Fit:     756  (total 756 atoms)
QMMM        :     756  (total 756 atoms)

If this is not helping you, please can you tell me what else you need?
Again, thanks.
cheers,
Andrea

In the absence of information about your ensemble (from your .mdp file or a
> description, hint hint) I'd guess it's because you've excluded all the
> non-bonded interactions for which you had non-zero parameters defined.
>
> Mark
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-- 
Dr. Andrea Minoia
Chemistry of Novel Materials
Uneversity of Mons, UMONS
Parc Initialis, Avenue Copernic 1
B-7000 Mons, Belgium
Mail: minoiaa at averell.umh.ac.be
Tel: +32 65 373859 Fax: +32 65 373861
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