[gmx-users] afm pull

[Frauke Meyer]

On Tue, 6 Jan 2004, Robert Vacha wrote:

> Hi all,
>   I have a problem with simple simulation using AFM pull code in version 3.1.5_pre1.
> My simulation consists of 4 atoms
> 1SOL     KR    1   0.697   0.647  15.809
> 2SOL     KR    2   0.697   0.647  15.282
> 3DRG     AR    3   0.697   0.647  20.000
> 4DRG     AR    4   0.697   0.647  10.000
> in normal NVE simulation argons stay(cut off =1nm) and kryptons oscilate in Lennard-Jones potential.
> But, if I connect my two argons by afm, argons stay and do not move.
> Could anyone give me some advice what can be wrong?
>
> Thanks,
> Robert Vacha
>
> ps: afm parameters are
> runtype                = afm
> reftype                = com_t0
> reflag                 = 1
> direction              = 0.0 0.0 1.0
> pullrate               = 0.00000000000001

Dear Robert,

this is a *really* small velocity, try to run with double precision.

Frauke


> forceconstant          = 5000
>
>
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--
Frauke Meyer
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
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