[gmx-users] g_select help

[Justin Lemkul]

On 9/25/13 12:24 PM, rajat desikan wrote:
> Basic question: How do I verify that the right atoms were chosen in the
> index file? There are a lot of atoms.
>

Pass the index file to trjconv and use it to parse out the atoms in the group 
from the original coordinate file.

-Justin

>
> 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
>>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================