[gmx-users] Fwd: self-assembly and box size

[Justin Lemkul]

On 11/14/16 5:11 PM, Mohsen Ramezanpour wrote:
> Dear Gromacs users,
>
> I have made an initial system with a number of molecules in a "large" box.
>
> Large means a box of size 50  50  50 nm?
>
> I am interested in the self-assembly process of molecules (parametrized in
> charmm36 ff) in the box.
>
> I expected pressure coupling to shrink the box quickly, but it seems it
> fails to do so. The simulation box did not change (ca. 0.5 nm in each
> direction) which seems strange to me.
>
> I have used four different P-couple schemes for 4 different type of
> self-assemblies:
>
> 1) isotropic
>
> pcoupl                  = berendsen
> pcoupltype           = isotropic
> tau_p                   = 5.0
> compressibility     = 4.5e-5
> ref_p                    = 1.0
>
>
> 2) semiisotropic
>
> pcoupl                 = berendsen
> pcoupltype           = semiisotropic
> tau_p                   = 5.0
> compressibility     = 4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0
>
>
> 3) anisotropic with *fix shape* of box (*but the size could change*)
>
> pcoupl                  = berendsen
> pcoupltype            = anisotropic
> tau_p                    = 5.0
> compressibility      = 4.5e-5  4.5e-5  4.5e-5   0       0       0
> ref_p                     = 1.0      1.0       1.0       0       0       0
>
> 4) anisotropic with *both size and shape able to change*
>
> pcoupl                  = berendsen
> pcoupltype           = anisotropic
> tau_p                   = 5.0
> compressibility     = 4.5e-5  4.5e-5  4.5e-5  4.5e-5  4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0     1.0     0       0       0
>
>
> Here are some other parameters in mdp file which might be useful for
> finding the problem:
>
> integrator              = md
> dt                         = 0.002
> nsteps                  = 50000
> nstlog                   = 1000
> nstxout                 = 1000
> nstvout                 = 1000
> nstfout                  = 1000
> nstcalcenergy       = 100
> nstenergy             = 1000
>
> cutoff-scheme      = Verlet
> nstlist                  = 20
> rlist                     = 1.2
> coulombtype        = pme
> rcoulomb             = 1.2
> vdwtype               = Cut-off
> vdw-modifier        = Force-switch
> rvdw_switch        = 1.0
> rvdw                    = 1.2
>
> tcoupl                   = berendsen
> tc_grps                 = Molecules   water_ions
> tau_t                     = 1.0    1.0
> ref_t                      = 355    355
>
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
>
> nstcomm                 = 100
> comm_mode            = linear
> comm_grps             = Molecules   WI
>

You shouldn't reset COM motion like this.

> refcoord_scaling        = com
>
> gen-vel                 = no
>
> I can make the initial system smaller, but I think starting from a large
> box would be better because it gives all the molecule enough freedom to
> move and assemble in better way.
>
> Is not it right to expect the p-couple shrink the box in nanoseconds? This
> was only for 100 ps but I expected more shrinkage of box. What do you think?
>

100 ps is nothing.

If you have a box full of water, as your settings above imply, you can't expect 
much of a change.  Why do you need the box to shrink, or why do you expect it 
to?  A box will only shrink a lot if there is substantial void space, e.g. 
intentional or due to a poor initial approximation of the system that requires 
equilibration.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================