[gmx-users] questions about AFM pulling

[Jian Zou]

Hi all,

Did anyone try using the same group as the ref_group and the pull_group?

I did a test for one spc water in a box and pulling it in one direction, 
using gmx-3.2.1,

my pull.ppa is as follows
verbose = yes
runtype = afm
group_1 = tip
reference_group = tip
reftype = com
reflag = 1
pulldim  = N N Y
afm_rate1 = 0.005
afm_k1 = 1500
afm_dir1 = 0 0 1
afm_init1 = 0 0 0

my index.ndx is
[ System ]
   1    2    3
[ SOL ]
   1    2    3
[ tip ]
   1

my water.gro is
ONE SPC H2O
  3
    1SOL     OW    1    .225    .275   -.866
    1SOL     HW1   2    .260    .258   -.774
    1SOL     HW2   3    .137    .230   -.878
   5.00000   5.00000   15.00000

but in pull.pdo,
0.000000 14.133964 14.133964 14.133964
0.001000 14.133964 14.133964 14.133969
0.002000 14.133964 14.133964 14.133974

I saw that at the time 0.00000, the position of the spc water has changed a 
great deal from that in water.gro.
Why?

I also use T P coupling and velocity generation in my mdp.
Am I wrong for this test run?

Thanks in advance.


Regards,

Jian Zou