[gmx-users] pull_distance

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 11 12:39:42 CET 2011

Алексей Раевский wrote:
> hi all.
>  I need your advice. I have marked several atoms from one chain and 
> several atoms from another chain (about 8 from each chain), they are 
> forming  5 h-bonding places, and now I want to stabilize the distance 
> between this chains during the MD. Can I use com pulling distance Y Y Y 
> for it with pull_k1 = 2000 and pull_init1 = with pull_rate1 = 0? Will it 
> hold the initial distance all the time and how many groups I have to 
> create? Will it be enough 2 groups (one with a selected atoms from first 
> chain and another with atoms from the second) in the index file or I 
> have to create sveral groups which will consist of a pairs of groups of 
> atoms involved in h-bonding? As I understood in this way I will handle a 
> center of mass, so the first variant is preferable. Is it true?

Yes.  Create one group for pull_group0, which is the reference (probably 
arbitrary in this case) and another for pull_group1.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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