[gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!

[Miguel Machuqueiro]

Dear users and developers,

In GROMACS 4.5.x when using "freeze groups" on a Protein in a 
Protein+Solvent system, I noticed that the coordinates of a few atoms 
(not many, but a few) are changed after a short period of MD (~0.2 ps). 
Of course, this is wrong!

Are there any options in MDP/GROMPP/MDRUN that can be originating this? 
Or it is some bug in the code?

A copy of my input file follows below.

Note that this version of GROMACS crashes if one uses "constraints" in 
LINCS together with "freeze groups". Hence the "constraints = none" line.

Any help is appreciated.

Regards,
Miguel

_____________

;       Input file
;
title               =  zzz
cpp                 =  /lib/cpp
define              =

integrator          =  md
tinit               =  0.0
dt                  =  0.002    ; ps !
nsteps              =  100
nstcomm             =  10
nstxtcout           =  500
xtc-precision       =  1000
nstxout             =  0
nstvout             =  0
nstfout             =  0
nstlog              =  0
nstenergy           =  500
nstcalcenergy       =  10
ns_type             =  grid

coulombtype         = Generalized-Reaction-Field
nstlist             =  5
rlist               =  0.8
rcoulomb            = 1.4
epsilon_rf          = 54.0
rvdw                = 1.4

vdwtype             = cut-off

; Energy monitoring
energygrps          =  Protein SOL

Tcoupl              =  v-rescale
tc-grps             =  Protein   SOL
tau_t               =  0.10      0.10
ref_t               =  310.0     310.0

; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

; lincs_order value of 8 works better than 4
constraint_algorithm=lincs
lincs_order         =  8
constraints         =  none
lincs-warnangle     =  90

freezegrps          =  Protein
freezedim           =  Y Y Y
energygrp_excl      =  Protein Protein


-- 
============================================
Miguel Machuqueiro
Department of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
Campo Grande, Edifício C8 (sala 8.5.47)
1149-016 Lisboa, Portugal
Tel.  : +351 217500112 (int.ext.28547)
Mobile: +351 967562285
E-mail: machuque at fc.ul.pt
www1: http://webpages.fc.ul.pt/~mamachuqueiro
www2: http://cqb.fc.ul.pt/intheochem
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