[gmx-users] thermostate and frozen atoms

[m b]

dear all
if I freeze atoms grompp wouldn't
let me use a thermostate (Nose Hoover) only
for the non-frozen atoms
If I include the frozen atoms as a seperate
group for temperature scaling my system explodes.
and the temperature given in ener.edr is nan.
no matter whether i set ref_t for the frozen
group to zero or some finite value.
(both does not happen for the same system
without thermostat)
I wonder if gromacs accounts correctly
for the reduced degrees of freedom ?
i'd appreciate any hints.
cheers
Michael

the md.mdp i use is given below

title                =  red122 001 6x10x1 slab + 1
styrene 10-mer MD
cpp                  =  /usr/bin/cpp
integrator           =  md
dt                   =  0.0002
nsteps               =  1000
nstcomm              =  1
comm_grps            =  xtal
nstxout              =  1
nstvout              =  0
nstfout              =  0
nstlog               =  10
nstenergy            =  10
constraints          =  hbonds
constraint_algorithm =  lincs
unconstrained_start  =  no
lincs_order          =  4
energygrps           =  xtal p01 p02 p03 p04 p05 p06
p07 p08 p09 p10
freezegrps           =  xtal
freezedim            =  Y Y Y
energygrp_excl       =  xtal xtal
pbc                  =  xyz
coulombtype          =  shift
vdwtype              =  shift
rcoulomb_switch      =  1.3
rvdw_switch          =  1.3
rcoulomb             =  1.5
rvdw                 =  1.5
rlist                =  1.3
nstlist              =  10
Tcoupl               =  nose-hoover
tc-grps              =  xtal polymer
tau_t                =  0.1 0.01
ref_t                =  300 300 
Pcoupl               =  no
gen_vel              =  yes
gen_temp             =  300.0
gen_seed             =  1799


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