[gmx-users] g_select help

Teemu Murtola teemu.murtola at gmail.com
Wed Sep 25 18:16:42 CEST 2013


On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> I have a dopc+50% cholesterol bilayer. I want to selectively choose the
> upper and lower leaflets. I used g_select the following way
> g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol
> and z>6' (6 is the COM of my box)
> I am getting the following error.
> Possible bug:
> one of the values for comparison missing
> g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol'
> works perfectly fine. What is the problem?

Your problem is that 'resname DOPC and resname Cholesterol' by definition
selects zero atoms. Try 'resname DOPC Cholesterol' instead. I will fix the
error message, but most likely not in any upcoming 4.6.x releases.

You may also find that unless you bilayer is very flat and static, you
don't get exactly the atoms you want. Try 'resname DOPC Cholesterol and
res_com z > 6'.

Best regards,

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