[gmx-users] Did -ndec stop working in 2016 releases?

[Mark Abraham]

Hi,

The g96 format is useful for this purpose.

Mark

On Fri, 21 Jul 2017 23:18 Caro Miguel <miguel.caro at aalto.fi> wrote:

> Thanks, that clarifies it (my bad!).
>
>
> --
> Dr. Miguel Caro
> Postdoctoral researcher
> Department of Electrical Engineering and Automation, and
> COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Email: mcaroba at gmail.com
> Work: miguel.caro at aalto.fi
> Website: http://mcaroba.dyndns.org
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: 22 July 2017 00:14:10
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Did -ndec stop working in 2016 releases?
>
>
>
> On 7/21/17 5:11 PM, Caro Miguel wrote:
> > Hello,
> >
> >
> > I am trying to extract trajectory data with more decimal places than the
> standard. I have been using gmx trjconv with the -ndec option to do this in
> the past. I am now using the 2016.3 release and the following command:
> >
> >
> > gmx trjconv -f md.trr -s md.tpr -o traj.gro -ndec 5
> >
> >
> > gives me a traj.gro file with only 3 decimal places, which is the
> default. I have also tested the 2016.1 release and I experience the same
> problem. Gromacs 5.1.4 behaves as expected.
> >
> >
> > Apparently trjconv understands -ndec since it's telling me "Setting
> output precision to 1e-05 (nm)", but the output .gro file is missing more
> decimal digits. Is this a (known) bug or should I be looking for problems
> with my installation?
> >
>
> This is by design.  Release notes are the first port of call!
>
>
> http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html#removed-variable-precision-gro-writing
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * 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 Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * 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.
>