[gmx-users] pull_distance

Алексей Раевский rayevsky85 at gmail.com
Fri Nov 11 12:09:26 CET 2011

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?

Thank you for responce


Nemo me impune lacessit*
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