[gmx-users] Reducing distance between atoms! PULL

Алексей Раевский rayevsky85 at gmail.com
Tue Feb 23 22:41:55 CET 2010

Sorry, I want to ask the same question I had a week ago. I need your advice

This is a part of article which describes methodology "...with respect to
the atomic distance between the carbonyl carbon of the substrate and the
oxygen atom of the identified nucleophilic water, a constrained MD
simulation was performed to investigate the mechanisms of the approach of
the water molecule. This simulation was started by using a harmonic
potential as the distance constraint, where the force constant was set to 5
kcal/mol å2. When the atomic distance was not reduced any further, despite
the presence of the harmonic potential in the MD simulation (at about 470
ps), the force constant was increased up to 200 kcal/mol å2; this was
exploited to mimic the first phase of a nucleophilic attack..all together
about 1ns"


"The atomic distance is 3.4 A, suggesting that this water molecule acts as a
nucleophile in the post-transfer editing reaction.."

I have to reduce distance between oxygen of H2O and carbon during
simulation, but H2O must be free enough for revolution around C. Index file
is ready for it. This is part of mdp.


; Pull type: no, umbrella, constraint or constant_force

pull = umbrella

; Pull geometry: distance, direction, cylinder or position

pull_geometry = distance

; Select components for the pull vector. default: Y Y Y

pull_dim = Y Y Y

; Cylinder radius for dynamic reaction force groups (nm)

pull_r1 = 1

; Switch from r1 to r0 in case of dynamic reaction force

pull_r0 = 1.5

pull_constr_tol = 1e-06

pull_start = yes

pull_nstxout = 1

pull_nstfout = 1

; Number of pull groups

pull_ngroups = 1

; Group name, weight (default all 1), vector, init, rate (nm/ps),

pull_group0 = C

pull_weights0 =

pull_pbcatom0 = 0

pull_group1 = H2O

pull_weights1 =

pull_pbcatom1 = 0

pull_vec1 = 0.0 0.0 1.0

pull_init1 = 3.4

pull_rate1 = 0.02

pull_k1 = 837

pull_kB1 = 837

Is everything ok with pull_vec1, pull_init1, pull_rate1 (if I put 0 atoms
will stay without any movement, but I suggest it will cause another result),
pull (umbrella is harmonical, constrains - no) and pull_geometry (in the
article was mentioned "distance" instead of "direction") ???

I did experiments with different changes in parameters...Waiting for your
comments. Thanks
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100223/e11c1181/attachment.html>

More information about the gromacs.org_gmx-users mailing list