On 8/8/13 6:43 PM, Bin Liu wrote:
Hi All,
I would like to restrain the COM of a molecule, say a protein, in my
simulation. I found the pull code can do the job. However, I am not sure
about several parameters in the .mdp file.
For example, if I want to restrain the COM of the protein in only z
direction, but not rigidly, I can specify the following parameters:
*; Setting A*
*pull = umbrella*
*pull-geometry = position*
*pull-dim = N N Y ; only applied to Z direction*
*pull-ngroups = 1
*
*pull-group1 = Protein*
*pull-start = no*
*pull-init1 = 3.0 3.0 3.0 ; suppose the initial position of the COM
is 3.0 3.0 3.0*
*pull-k1 = 50*
I am not confident about my understanding of the settings. Here I didn't
specify *pull-group0*. Therefore the position of the reference point is 0.0
0.0 0.0. But *pull-init1* moves the reference point to *3.0 3.0 3.0. *I
What information makes you say this? What is the grompp output?
don't know the reasonable range for *pull-k1 *too. I want the COM can only
have a small deviation from its initial position. Is 50 too large or too
small?
That depends on your definition of "small." I would suspect that a pull_k1
value of only 50 is rather weak. There are no hard and fast rules here,
unfortunately.
And I figured out another approach.
*; Setting B*
*pull = umbrella*
*pull-geometry = position*
*pull-dim = N N Y ; only applied to Z direction*
*pull-ngroups = 1
*
*pull-group1 = Protein*
*pull-start = yes*
*pull-k1 = 50*
*
*
The GROMACS manual says *pull-start=yes *adds the COM distance of the
starting conformation to *pull-init. *Does it mean Setting B is equivalent
to Setting A? If I set *pull-geometry= position, *does *pull-start=yes *add
the initial position of the COM to *pull-init* as a vector? If it's true,
then I don't need to calculate the initial position of the COM.
With pull_geometry = position, restraints are determined based on pull_vec1,
which defaults to (0,0,0) so the default may be appropriate.
Out of curiosity, why is it necessary to restrain the protein in a given
position? If there's a homogeneous solvent around it, the restraint is
pointless and does cause problems with COM motion (as noted in the manual). If
there are other molecules in the system, you can probably define a better
reference point.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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