[gmx-users] g_select help
rajatdesikan at gmail.com
Wed Sep 25 18:22:37 CEST 2013
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:
> On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan <rajatdesikan at gmail.com
> > 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
> > 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,
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
More information about the gromacs.org_gmx-users