[gmx-users] g_select

[Josip Lovrić]

Hello,

I managed to create notattached group but now it is not recognizing system
group when I compile it with gromp.
I get this answer:

Fatal error:
Group system referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

This is my grompp line:
grompp_mpi -f md.mdp -c nacl_palm_md_224.gro -p topol_nc.top -o
nacl_palm_md_224_na.tpr -n select.ndx

group system is defined like this in .top file:

[ system ]
; Name
NaCl

P.S.
Feel free to ask me more information, I am quite new in gromacs and I am
not sure if I am giving you all the information.



2014-03-25 17:31 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 3/25/14, 12:10 PM, Josip Lovrić wrote:
>
>> Dear GROMACS community,
>>
>> I am trying to index some molecules with g_select. I have system of
>> carboxylic molecules(group named MOL) forming monolayer on NaCl surface.
>> Some of the molecule are attached to surface and some not. With g_select I
>> want to select molecule which are not attached to
>> surface. molecules which are not attached are more far from surface so I
>> am
>> using that fact.
>> This is line of g_select
>>
>> g_select_mpi -sf select.dat -f nacl_palm_md_224.xtc -s
>> nacl_palm_md_224.tpr
>> -b 4000 -e 4000 -on select.ndx
>>
>> and select.dat is
>>
>> not_attached = group "MOL" and not within 2 of resname Na;
>> not_attached;
>>
>> Gromacs return me this answer selection parser: invalid selection
>> 'not_attached = group "MOL" and not within 2 of resname Na'
>>
>> When I use "resname MOL" instead of "group" it is working, but then in
>> index file I only have numbers of atoms ant that is useless for me.
>> I want to have molecules which are not attached to surface.
>> So obviously gromacs is not recognizing my MOL as a group, which is
>> strange
>> because MOL is recognized as a energy group in my .mdp file.
>>
>>
> If you're using a custom group, then you need to pass an index file to
> g_select that specifies that same group.  If it's a default group, this
> shouldn't be an issue.  You can get around the above problem of incomplete
> residues by starting the selection with "same residue as" to select the
> whole residue that contains any atoms that satisfy the selection.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
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