[gmx-users] g_select help

[rajat desikan]

Basic question: How do I verify that the right atoms were chosen in the
index file? There are a lot of atoms.


On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Thank you very much. My bilayers were initially built with packmol which
> is probably why z>6 worked. I will keep this in mind.
>
>
> On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola <teemu.murtola at gmail.com>wrote:
>
>> Hello,
>>
>> 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,
>> Teemu
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>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore