[gmx-users] 3.2.0_beta pull code: bug or feature?

Frauke Meyer fmeyer at ix.urz.uni-heidelberg.de
Fri Jan 9 07:25:01 CET 2004


I am testing the AFM pull code of the 3.2.0 beta version, and am happy to
see all the new features, like different velocities/force constants for
each pull group and choice of the initical spring position - nice! But I
wonder, how the spring is dislocated.

So far (3.1.4), the spring is moved by a constant distance each
step, corresponding to constant velocity in afm experiments. In the
3.2.0 version it now reads:

        pull->grp[i].spring[m] = pull->grp[i].AfmInit[m] + pull->ref.x_unc[m] +

The spring position is calculated relative to the reference group and
(rate * time) is added each step. This is equal to what the pull code used
to do only if the reference group is fixed. And: the initial force is not
zero but (force constant times (distance between pull and reference
group)). Which should rather be defined in the parameter file as initial
spring position afm_init1. Is that wanted or a bug? Or do I miss

I changed the lines above in pull.c to

    if (step != 0)
          pull->grp[i].spring[m] += pull->grp[i].AfmVec[m]*pull->grp[i].AfmRate*dt +

and now can reproduce the 3.1.4 results, if  refgroup=pullgroup.

parameters for 3.2.0:
verbose = yes
runtype = afm
group_1 = bom
reference_group = bom
reftype = com
reflag = 1
afm_dir1 = 0.0 0.0 1.0
reverse = from_reference
update = 1
afm_rate1 = 0.2
afm_k1 = 500
pulldim                  = N N Y

parameters for 3.1.4:
verbose = yes
runtype = afm
group_1 = bom
reference_group = ala128
reftype = com
reflag = 1
direction = 0.0 0.0 1.0
reverse = to_reference
update = 1
pullrate = 0.0004
forceconstant = 500


Frauke Meyer
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Shanghai 201203
Tel: +86 21 50806600*1201, Fax: +86 21 50806600*1205
http://www.dddc.ac.cn, e-mail:frauke.meyer at mpi-bpc.mpg.de

More information about the gromacs.org_gmx-users mailing list