On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote:
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.
Indeed, because imposing the constraints can perturb the (frozen)
positions slightly, leading to numerical issues... Similarly, if you
couple the frozen groups to a heat bath, you're going to find that
they're not actually frozen. And pressure-coupling is not known to
always play nicely with frozen groups either (search the archive for more).
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
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