[gmx-users] Error select a group gmx_density

[Justin Lemkul]

On 2/15/17 11:18 AM, Poncho Arvayo Zatarain wrote:
>
>
> Ok, thanks Justin. But i have one more question: What do you mean with syntax
> make_ndx? Is the way the command is writting: gmx_gpu density -ng 4 -f
> npt06.xtc -s npt06.tpr -o density.xvg? Is there anoher way to wrtie the
> command for density?
>

My comment was not anything related to the command itself.  You were trying to 
use & and | operators to merge groups.  That's make_ndx syntax.  It's not 
something you can do with analysis tools.  Selections made (when choosing from a 
list of available groups) with analysis tools are done with a single number or 
group name.

-Justin

> ________________________________ De:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> en nombre de Justin
> Lemkul <jalemkul at vt.edu> Enviado: miércoles, 15 de febrero de 2017 08:02 a.
> m. Para: gmx-users at gromacs.org Asunto: Re: [gmx-users] Error select a group
> gmx_density
>
>
>
> On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote:
>>
>> Hello Gromacs users: I´m trying to obtain the density og a mixed membrane
>> plus a protein. I use the command line:  gmx_gpu density -ng 4 -f npt.xtc
>> -s npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION
>> 5.0.4 (single precision)
>>
>> Select 4 groups to calculate density for: Group     0 (         System)
>> has 58780 elements Group     1 (          Other) has 58780 elements Group
>> 2 ( PROTEIN) has   576 elements Group     3 (           DPPC) has 16640
>> elements Group     4 (           DPPE) has 15488 elements Group     5 (
>> TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC'
>> Select a group: Error: No such group '&' Select a group: Selected 4:
>> 'DPPE' Select a group: Error: No such group '&' Select a group: Selected
>> 2: 'PROTEIN' Select a group: Error: No such group '&' Select a group:
>> Selected 5: 'TIP3' Last frame       5000 time 210000.000
>>
>> Read 5001 frames from trajectory. Calculating density
>>
>> Is there anything wrong with the command line or with Select a group:
>> Error: No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the
>> same error but with | instead &? What about the Last frame 5000 time
>> 210000.000?
>
> You can't use make_ndx style syntax with gmx density.  You should be
> prompted for 4 selections, individually.  Otherwise, just calculate the
> density of each group separately.
>
>> Why 5000 and not 210000.000?. Also, and .xvg file is generated Thanks
>>
>
> What should the time be?  What is printed to the terminal is just a running
> indicator of progress; it is not a definitive statement of the contents of
> the trajectory.  For that, use gmx check (or look in the .xvg file to see the
> time values).
>
> -Justin
>
> -- ==================================================
>
> Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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