On 10/12/16 8:15 AM, Fabian Knoch wrote:
Dear users,

I got some questions concerning the pull code (Gromacs 5.1.2) more precisely
about the constant force protocol. I searched already quite a bit but couldn't
find any satisfying answers.

If I understand it correctly the two major options one has to set for the
pull-geometry is "distance" or "direction".

For "distance" I have to specify two groups and Gromacs calculates the vector
connecting both groups and applies the force along the connecting vector.
Hence, the simulation box has to be more than twice as large as the length of
the connecting vector because otherwise the vector cannot be uniquely determined
(minimum image convention).

For the second option "direction" one has to specify a vector "pull-coord1-vec "
along the force will be applied.

My first question is what's the difference between option "distance"  with
"pull-coord1-dim =  N N Y" and "direction" with "pull-coord1-vec = 0 0 1" ? If I
understand the mainual correctly, these two options should give identical 
results.

Now concerning my problem:

For my pulling simulations (pulling of a protein) I cannot choose "distance"
because then the box size becomes too large and I simply have too much water in 
it.

So I need to take the "direction" option with "pull-coord1-vec = 0 0 1" (pulling
in z-direction) and further introduce a position restraint (C_alpha N-terminus)
ensuring that the protein is not floating around too much.

Now after I run the simulation for a bit, gromacs returns an error saying that
the distance is larger than 0.49 the box size and I should consider using
"pull-geometry = direction-periodic".

Could anyone explain to me why I receive this error message. I don't understand
what distance gromacs is referring to. I assume the distance between the pulling

The restraint distance is always the minimum periodic distance. If your restraint length goes to half the shortest box length, you get discontinuities in the pulling. Hence GROMACS exits with an error rather than continuing on.

group and the point (0,0,0), though. Second, I don't understand the distance
reference in general as I specified "pull-geometry =direction". For my
understanding the box size should not matter as a constant force (with fixed
direction) is simply applied to a reference group.  It is conceptually identical
to a constant electric field (in fixed direction) which acts only on a reference
group. It should only be important to make the box large enough to avoid
self-interactions.

To bypass this error I have to set "direction-periodic" but then I cannot use
isotropic pressure coupling anymore and thus have to use semiisotropic pressure
coupling.


Or you can use NVT.

So my questions sum up to why is not possible to use pull-geometry = direction
with a box size protein length + say 4 nm and isotropic pressure coupling ?


It should be, as long as your reaction coordinate is always less than 2 nm, or less than 0.49*(whatever the box vector is when applying pressure coupling).

-Justin

Attached are two pull-code snippets from my .mdp file:

(i) "pull-geometry = direction" ----> Not working

pull = yes
pull_ngroups = 1
pull_ncoords = 1
pull-coord1-groups = 0 1
pull_group1-name = pull-atom
pull-coord1-type = constant-force
pull-coord1-geometry = direction
pull-coord1-vec = 0.0 0.0 1.0
pull-coord1-k = -300

(ii) "pull-geometry = direction-periodic" ---> working

pull = yes
pull_ngroups = 1
pull_ncoords = 1
pull-coord1-groups =0 1

pull_group1-name = end-atom
pull-coord1-type = constant-force

pull-coord1-geometry = direction-periodic
pull-coord1-vec = 0.0 0.0 1.0
pull-coord1-k = -300

pcoupltype          = semiisotropic
tau_p                   = 2.0
ref_p                    = 1.0 0
compressibility    = 4.5e-5 0


Thank you

Fabian



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

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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