[gmx-users] CONSTRAINED SIMULATIONS
gpellicane at unime.it
Sun Jan 24 19:52:06 CET 2010
I don't think it is something related to pbc because my solutes are well
inside the simulation box (as I told you before I visualize them via a movie
while the simulation proceeds).
Nor it is something related to the barostat because I saw that warning
and in order to try to see it work I decided to do NVT simulations.
However, the problem persists.
I'm using angle restraints on the "pulled" group in order to preserve its
orientation with respect to the reference group. Could this be the problem?
2010/1/24 <chris.neale at utoronto.ca>
> Dear Giuseppe:
> OK, those are the forces. They seem pretty huge and massively fluctuating,
> although I use umbrella sampling myself so this might be quite normal for
> constraint sampling (something for you to look into).
> The only thing that comes to mind is that your running up against a pbc
> problem in determining either the center of mass of each protein prior to
> solving the constraint or that your constraint is oscillating about
> different "shortest distances" over different images.
> The gmx3 manual also says this:
> Another limitation is connected with pressure scaling. When pressure
> scaling is used, the shortest distance between the pull groups and the
> reference group should be within in the central unit-cell, not to periodic
> images of the pull groups. Otherwise the pressure scaling will affect the
> reference distances and thus also the forces. The exception is constraint
> pulling with constraint distance? > 0, this will work correctly with
> pressure scaling under all conditions.
> So here's what I recommend:
> 1. create a system that has no water so that it runs faster.
> 2. Use the sd integrator so that you get some random noise.
> integrator = sd
> tc_grps = System
> tau_t = 1.0
> ld_seed = -1
> ref_t = 300
> gen_temp = 300
> gen_vel = yes
> unconstrained_start = no
> gen_seed = -1
> 3. see if you can reproduce the problem.
> 4. Make the box much bigger and center your solutes (trjconv -center -pbc
> mol) so that you need not worry about pbc problems.
> 5. see if you can reproduce the problem.
> -- original message --
> Got it!
> Ok, first lines:
> # CONSTRAINT 3.0
> # Component selection: 1 1 1
> # nSkip 1
> # Ref. Group 'protein_b'
> # Nr. of pull groups 1
> # Group 1 'protein_a' Pos. 3.099513 2.982803 3.377482
> 0.000000 -787.501479
> 0.002000 -271.159600
> 0.004000 -1147.351351
> 0.006000 -108.722797
> 0.008000 -97.813955
> 0.010000 58.592018
> 0.012000 428.034442
> 0.014000 1022.187858
> 0.016000 -60.867559
> 0.018000 334.483373
> 0.020000 1328.818408
> 0.022000 940.307012
> 0.024000 368.857413
> 0.026000 1680.598490
> 0.028000 857.879861
> 0.030000 362.426529
> 0.032000 1717.334105
> 0.034000 810.192387
> 0.036000 105.655760
> 0.038000 1048.031839
> 0.040000 484.148742
> 0.042000 1312.769160
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