[gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!
machuque at fc.ul.pt
Mon Nov 15 15:11:14 CET 2010
Dear Mark, users and developers...
Indeed, the source of the problems comes from both the constraints and
the pressure bath. The temperature bath did not seem to interfere.
Now, the problem is clear, to remove constraints is not only compulsory
but also recommendable for such simulations.
However, the pressure bath (which is the major source of the problems)
should not play such a role. This is a limitation of the current
implementation of GROMACS or just a plain BUG.
I think most people would agree that one should not be limited to NVT
simulations when using freeze groups.
A previous version (3.2.1) that we have been using in our group was
completely immune to both pressure bath and constraints when simulating
a frozen protein in water. As far as I remember, this older version did
a normal step integration with all its requisites and, in the end, just
took back the previous positions for the frozen group (protein).
My question remains...
Will we be able to use freeze groups together with a NPT simulation in
Any comments from the developers are welcome...
On 11/11/2010 1:07 AM, Mark Abraham wrote:
> 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.
>> ; 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
>> lincs_order = 8
>> constraints = none
>> lincs-warnangle = 90
>> freezegrps = Protein
>> freezedim = Y Y Y
>> energygrp_excl = Protein Protein
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