[gmx-users] CONSTRAINED SIMULATIONS

[Giuseppe Pellicane]

Dear Chris:

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?

Cheers,

 Giuseppe

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.
>
> Chris
>
> -- 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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