[gmx-users] Pull code with dummy atom as reference - not working
jalemkul at vt.edu
Tue Jul 29 01:23:03 CEST 2014
On 7/28/14, 7:18 PM, Stella Nickerson wrote:
> 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.
Just split the run into two, one with a suitable pull_k1 for the first liquid,
and a different pull_k1 or pull_rate1 for the second. If the sole purpose for
the SMD is just to generate configurations, there's nothing saying the SMD has
to be continuous.
> Thanks again!
> 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
>> Gromacs Users mailing list
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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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