[gmx-users] AFM pulling of two groups

[Ester Chiessi]

Hi all.

I'm trying to use AFM pulling to prepare my starting structure (with
Gromacs 3.2.1).
After a fail in working with the reference group left blank ( is it a bug?)
I tried to pull simoultaneously two groups relative to the reference group.

I can't understand why, but it seems that pulling is only on the group_1,
although I give also a group_2.

There is also a strange thing: the first element of the group seems to have
an atom number reduced of a unity ( i.e. 144 instead of 145 ) and the index
file is correct.

Could anyone give me a suggestion?
Thanks.

Ester

In the following you can find part of the output:

from file pullout.ppa:
;
;       File 'pullout.ppa' was generated
;       By user: incrm401 (30143)
;       On host: sp011
;       At date: Wed Jan 19 11:13:47 2005
;
; GENERAL
verbose                  = no
Skip steps               = 1
; Runtype: afm, constraint, umbrella
runtype                  = afm
; Groups to be pulled
group_1                  = a_145-416
group_2                  = a_705-976
group_3                  =
group_4                  =
; The group for the reaction force.
reference_group          = a_1265-1536
.........

from output of mdrun:

**************************************************
                         PULL INFO
**************************************************
RUN TYPE: Afm
REFERENCE TYPE: center of mass of reference group
Looking for group a_145-416: found group a_145-416: 272 elements. First: 144
Looking for group a_1265-1536: found group a_1265-1536: 272 elements.
First: 126
4
Initializing pull groups. Mass of group 0: 2995.631
Initial coordinates center of mass:   25.774   25.853    0.108
Initializing reference group. Mass: 2995.631
Initial coordinates center of mass:    9.012    0.059    8.994

Pull rate: 1.000000e-05 nm/ns. Force constant: 1.000000e+02 kJ/(mol nm)
Pull direction:    0.797   -0.431   -0.423
Started mdrun on node 0 Wed Jan 19 11:13:48 2005
Initial temperature: 303.081 K
.........

from pull.pdo:

# AFM   3.0
# Component selection: 1 1 1
# nSkip 1
# Ref. Group 'a_1265-1536'
# Nr. of pull groups 1
# Group 1 'a_145-416'  afmVec 1.000000 1.000000 0.000000  AfmRate 0.000010
AfmK
 100.000000
#####
..........



Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
Via della Ricerca Scientifica
00133 Roma
tel. +39 06 72594462
fax  +39 06 72594328
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm