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
--
---------------------------------------------------
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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