[gmx-users] Trjconv problem invalid argument

[Justin Lemkul]

On 2/14/17 1:08 PM, Poncho Arvayo Zatarain wrote:
> Ok, so should i write trjconv before -ng 3, like gmx_gpu density trjconv -ng 3 -f file.xtc -s file.tpr -o out.xtc -skip 100 or donde write -ng in the command line?
>

There is no invocation of trjconv if you're trying to calculate the density. 
"gmx trjconv" is a command with its own set of options, while "gmx density" is a 
different command that calculates the density.  You can't mix the two.

-Justin

>
> Thanks
>
> ________________________________
> 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: martes, 14 de febrero de 2017 09:53 a. m.
> Para: gmx-users at gromacs.org
> Asunto: Re: [gmx-users] Trjconv problem invalid argument
>
>
>
> On 2/14/17 12:45 PM, Poncho Arvayo Zatarain wrote:
>>
>>
>> Hello Gromacs users: I want to obtain the density of a system using the
>> command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip
>> 100, but the following error appears: Invalid command argument: trjconv. What
>> is wrong with trjconv? I am using gromacs 5.0.3
>>
>
> Nothing is wrong with trjconv, but your command is attempting to execute trjconv
> as an argument to gmx density -ng, which is complete nonsense.
>
> -Justin
>
>
> --
> ==================================================
>
> 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
> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul>
>
> Welcome to my site! - University of Maryland, Baltimore<http://mackerell.umaryland.edu/~jalemkul>
> mackerell.umaryland.edu
> Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above.
>
>
>
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
> www.gromacs.org
> This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page.
>
>
>
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists>
> www.gromacs.org
> The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them:
>
>
>
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> gromacs.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> maillist.sys.kth.se
> gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users
>
>
>

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

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

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