[gmx-users] questions about AFM pulling
fmeyer at iris3.simm.ac.cn
Mon Dec 13 06:11:28 CET 2004
Hi Jian Zou,
what are your box dimensions - about 14nm? You start at the corner of
the box, no, even outside the box (z<0), pull.pdo gives the dimensions
of the copy of your system *in* the box.
First center the water in your box.
On Mon, 2004-12-13 at 11:06, Jian Zou wrote:
> 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 ]
> my water.gro is
> ONE SPC H2O
> 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.
> I also use T P coupling and velocity generation in my mdp.
> Am I wrong for this test run?
> Thanks in advance.
> Jian Zou
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