On 4/29/13 8:34 PM, Mark Abraham wrote:
I do not see that the caption to figure 4.8 implies a "reference" atom. It
Sorry, loose terminology after a long day. "Reference atom" is a poor choice.
What I meant was with respect to the way pdb2gmx constructs impropers - the
central atom (i.e. the one around which planar geometry is to be observed) is
written first as atom i.
talks merely about the angle between planes i-j-k and j-k-l. That angle is
signed and the sign is significant for equation 4.60. Does the sign of the
angle differ from that between l-k-j and k-j-i? I think not, but it's way
too late here for me to wrap my right-hand-rule for cross-products around
that one! :-)
Likewise.
I created a simple test case that confirms that for _exact reversals_ of atom
numbers within an improper listing (i.e. 1 2 3 4 vs. 4 3 2 1), the energy
associated with the improper term does not differ significantly. Minor
differences noted, but within error, hence standard MD at play :) For any other
order, things go haywire.
-Justin
On Tue, Apr 30, 2013 at 2:06 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/29/13 8:00 PM, Mark Abraham wrote:
On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul <jalem...@vt.edu> wrote:
Please start a new thread if you're going to introduce a new topic. I
have changed the subject to something more relevant.
On 4/29/13 4:23 PM, lloyd riggs wrote:
*Dear All,*
*Doing a water/temp energy minimization just for a figure with a large
molecule
that has several connected parts, I ran into a bizzar question.*
*So I found its possible by accident to define improper dihedrails
forwards and
backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1.
My
question is, if your topology has this, does it affect the calculations
(angle
energy or other)?*
Yes, it does. For impropers, the order matters. In the two examples,
you
are specifying different properties. With "1 2 3 4," you are saying that
atom 1 is planar and atoms 2, 3, and 4 are the atoms around it that
govern
its planarity. With "4 3 2 1," you are saying atom 4 is the planar
center,
with atoms 1, 2, and 3 similarly governing its planarity.
I didn't know that. A quick look in the manual didn't reveal where we have
that documented. Do we?
(Obviously, it is only applicable to harmonic-type improper dihedrals.)
I have always interpreted Figure 4.8 to imply that if one changes the
order of the atoms (ai, aj, ak, al in the topology), the planes defined
around the reference atom would be different for a given set of 4 atoms in
different order. Is this not the case? I haven't gone into the code to
see how the topology is interpreted.
-Justin
--
==============================**==========
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Department of Biochemistry
Virginia Tech
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