[gmx-users] Pull code with dummy atom as reference - not working
stella.nickerson at gmail.com
Tue Jul 29 01:18:10 CEST 2014
Thanks, using direction geometry worked well. Since you seem to be very
knowledgeable about this particular area, would you mind another
question--When my particle passes through the less viscous to the more
viscous liquid, it hovers at the interface for several picoseconds before
bursting forward, shoving molecules out of its way. I've tried increasing
pull_k1. If I increase it too high, it messes up pressure scaling and
chaos reigns, but k1 < 3000 doesn't seem to get it through the viscous
liquid. Is the pull code just not practical for this system? Because if
so, I'm going to have to figure out another way to generate a PMF.
On Wed, Jul 23, 2014 at 1:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/23/14, 4:04 PM, Stella Nickerson wrote:
>> I want to pull a carbon particle (170 atoms in a lattice) across an
>> interface between Liquid A and Liquid B. The particle starts out in
>> A with the center of mass at about x = 2.5 y = 2.5 z = 2.5. The
>> liquid-liquid interface is at about z = 5. I want to pull the particle in
>> a straight line in the positive z direction. So I put a dummy atom (no
>> interaction perameters) in Liquid B at x = 2.5 y = 2.5 z = 7.5 to use as a
>> reference. I put the dummy atom in a freeze group to keep it from moving.
>> This is my pull code in my .mdp file, plus the freeze group code (DMY is
>> the dummy atom, DNP is the carbon particle):
>> ; Pull code
>> pull = umbrella
>> pull_geometry = distance ; simple distance increase
>> pull_dim = N N Y
>> pull_start = yes ; define initial COM distance > 0
>> pull_ngroups = 1
>> pull_group0 = DMY
>> pull_group1 = DNP
>> pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns
>> pull_k1 = 1000 ; kJ mol^-1 nm^-2
>> ; Define dummy atom as freeze group
>> freezegrps = DMY
>> freezedim = Y Y Y
>> At first I used a negative pull rate because this tutorial (
>> says to use a negative pull rate if you want to decrease the distance
>> between pull_group0 and pull_group1. But instead of moving in a straight
>> line in the positive z direction, the particle moved in the negative z
>> direction at an angle (could this be because of periodic boundary
> The negative pull_rate doesn't make sense when the reference group has a
> larger z-coordinate than the pulled group. Perhaps I need to clean up that
> language in the tutorial. Here, a positive pull_rate or "direction"
> geometry with pull_vec1 specified explicitly should do what you want.
> When I tried to use a positive pull rate the particle just shuffled around
>> in a little x-y circle.
> Try direction or position geometry with an explicit pull vector. You may
> also need to toy with the value of pull_k1, depending upon the viscosity of
> your liquids (resisting the movement of a large particle).
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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