[gmx-users] Steered MD: Gromacs 4.0

Matthew L. Danielson mldaniel at purdue.edu
Thu Mar 11 00:11:14 CET 2010


I am having some trouble using the COM pulling code (Gromacs 4.0). I will try to describe the problem as 
best I can and hopefully someone will be able to point me in the right direction!

Basically what I would like to do is pull a ligand (LIG) along a specified 
path from the interior of a protein to the exterior (Steered MD simulation). 
Using the following .mdp file I was able to pull the ligand, but it did not travel 
along the path that I thought it would (ie along the vector specified in pull_vec1). 

Pull section of my md.mdp file:

pull			= umbrella
pull_geometry 		= position
pull_dim 		= Y Y Y

pull_r1 		= 1
pull_r0 		= 1.5
pull_constr_tol		= 1e-06
pull_start 		= no
pull_nstxout 		= 10
pull_nstfout 		= 1
pull_ngroups 		= 1

pull_group0 		= 
pull_weights0 		=
pull_pbcatom0 		= 0
pull_group1 		= LIG 
pull_weights1 		=
pull_pbcatom1 		= 0
pull_vec1 		= -31.07-15.37 9.89
pull_init1 		= 43.416 66.914 40.125
pull_rate1 		= 0.001
pull_k1 		= 500
pull_kB1		=

I specified pull_vec1 as the vector I would like to pull the ligand along (ie -x,-y,+z).  
Looking at the simulation in VMD the ligand traveled in the (+x, +y, +z) direction. 

In this trial I specified pull_init1 as the point I would like the spring to be attached to the ligand.

I have read the gromacs 4.0 manual and many of the posts online, but I still cannot seem to figure out what values are required in the parameter file. 
I know the following pieces of information, but I don't know how/if they fit into the parameter file:

1. The point where I would like the spring to be attached to the ligand
2. The vector along which I would like the ligand to travel
3. The distance between a reference atom in the protein and the desired spring attachment point on the ligand

Anyone have any ideas of what i am missing or doing wrong?  Or if I am missing some fundamental concept here?

Matt Danielson


Matthew L. Danielson

Graduate Student of Medicinal Chemistry & Molecular Pharmacology
College of Pharmacy, Nursing, and Health Sciences
Purdue University
575 Stadium Mall Drive
West Lafayette, IN 47907-2091

(765)496-6643 office 

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