On 5/9/15 9:52 PM, Eric Dybeck wrote:
Hello All,
I am looking to run a set of simulations in which molecules are slowly
restrained to their COM positions. To provide some context, I am going to
melt a solid, and I would like to restrain the molecules first so that they
remain in their lattice position as the melting takes places.
I believe that I can achieve this using the pull code, although I've never
used this feature in gromacs before. As I understand it, the settings in my
.mdp file should look something like:
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y ; 3D harmonic restraints
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1 ; This may need to be the number of molecules
pull_group0 = ; Reference molecule
pull_group1 = ; Restrained Molecule
pull_rate1 = 0 ; No pulling rate, I am just keeping them in a
fixed position
pull_k1 = 1000 ; This number I will vary along the alchemical
path
In most of the pull code examples that I've seen, one atom group in the
simulation is being pulled away from another atom group also in the
simulation. In this case, the groups in the simulation will need to get
pulled toward a fixed 'reference' point that is defined based on an initial
configuration that I can supply. Is this doable? Obviously I could also
give an absolute (X,Y,Z) coordinate of the desired COM based on the initial
.gro file if that is easier to do.
The reference coordinates can be constant with grompp -r, which overrides -c for
the purpose of defining the reference for the restraint. In your case, though,
you're effectively trying to restraint a molecule/group to itself in some other
state. I doubt the pull code deals elegantly with this situation. In theory,
you could define a duplicate for each atom that is just a dummy, with some fixed
position, that defines a reference for each pulled group. Effectively, each
molecule is a "ghost" of itself. Then you can assign each restraint. I have no
idea if that will work; just a guess based on "typical" use of the pull code.
Also, I will need to restrain all the molecules in the solid, rather than
just a single molecule. Is it possible to have ~100 groups harmonically
restrained with the Pull code?
Probably, but it's likely to be very inefficient.
If you're trying to melt a solid, wouldn't something like a sheer force using
acc-grps be more appropriate?
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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