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 <rajatdesi...@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.murt...@gmail.com>wrote:
Hello,
On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan <rajatdesi...@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
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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
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