[gmx-users] rare huge forces in constraint simulation with direction_periodic

[Jochen Hub]

Sorry, I forgot: I used gmx version 4.5.5-dev.

Jochen

Am 6/25/12 3:53 PM, schrieb Jochen Hub:
> Hi,
>
> I am running a constraint simulation, with 12 molecules restrained with
> respect to the center of mass of a lipid membrane. During 5ns of
> simulation, I get a few frames (e.g. 10 or so) with huge forces on all
> molecules, whereas the forces in all other frames are fine. When looking
> at the simulation, nothing looks spurious. There are no LINCS warnings
> or so. Here is an example. Note the large forces at t=385.32. In
> pullx.xvg, the molecules are not set to the correct constrained position
> in the problematic frame:
>
> pullf (12 pull groups, 4 pull shown here):
>     385.12   6.65942   325.524  -122.863  -156.645 ...
>     385.16   312.699   498.147  -282.365   66.9014 ...
>      385.2   271.748   581.749   42.3289  -48.3744 ...
>     385.24   256.169   481.929  -147.006  -163.566 ...
>     385.28   360.289   435.808  -128.435   126.654 ...
>     385.32   27214.7   27461.9   26817.9   27025.9 ...
>     385.36   140.386   129.482   359.494  -5.16442 ...
>      385.4 -0.0698604  -457.767    -68.48    173.24 ...
>     385.44  -323.406  -161.396  -187.093   396.581 ...
>     385.48  -427.383   19.5112  -144.655  -95.9228 ...
>     385.52  -102.406   61.0266  -758.817   35.7622 ...
>
> pullx (12 pull groups, reference group + 4 pull groups shown here). The
> four molecules shown here are restrained at z=-1.831 with respect to the
> lipid membrane:
>     385.12    3.5217    -1.831    -1.831    -1.831    -1.831 ...
>     385.16    3.5217    -1.831    -1.831    -1.831    -1.831 ...
>      385.2    3.5216    -1.831    -1.831    -1.831    -1.831 ...
>     385.24   3.52142    -1.831    -1.831    -1.831    -1.831 ...
>     385.28   3.52231    -1.831    -1.831    -1.831    -1.831 ...
>     385.32    3.5222  -1.83208  -1.83208  -1.83208  -1.83208 ...
>     385.36   3.52209    -1.831    -1.831    -1.831    -1.831 ...
>      385.4   3.52192    -1.831    -1.831    -1.831    -1.831 ...
>     385.44   3.52175    -1.831    -1.831    -1.831    -1.831 ...
>     385.48   3.52165    -1.831    -1.831    -1.831    -1.831 ...
>     385.52   3.52156    -1.831    -1.831    -1.831    -1.831 ...
>
>
> I used gmx 4.5.5-dev, the relevant mdp options are (pressure coupling in
> z is switched off):
> pull                     = constraint
> pull_geometry            = direction_periodic
> pull_dim                 = N N Y
> pull_constr_tol          = 1e-06
> pull_ngroups             = 12
> pull_group0              = refgroup
> pull_weights0            =
> pull_pbcatom0            = 54
> pull_group1              = Solute_Layer0_Channel0
> pull_weights1            =
> pull_pbcatom1            = 0
> pull_vec1                = 0.0 0.0 1.0
> pull_init1               = -1.8310
> pull_rate1               = 0
> ...
>
> Apart from this, I use the md integrator, LINCS for all bonds, V-rescale
> T-coupling (tau=5ps), pressure coupling in the xy plane only
> (compressibility = 4.5e-5 0 with Pcoupltype = semiisotropic), LJ cutoff
> at 1nm, PME, so normal settings.
>
> Did anyone see a similar behavior? Or any hints what one could try? Bug
> or feature of the constraint algorithm?
>
> Many thanks in advance,
> Jochen
>
>
>

-- 
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Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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