[gmx-users] command line with gangle

[Teemu Murtola]

By far the simplest method is to just pass your selections as command line
arguments, without any files:

  gmx gangle ... -group1 0 -group2 3

One goal for the selection implementation was that it's not necessary to
play around with complicated redirections to automate things.
On Mar 20, 2015 3:52 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 3/20/15 11:49 AM, ABEL Stephane 175950 wrote:
>
>> Hello all,
>>
>> I have a stupid question :
>>
>> I would like to use gangle (v5.0.4) with the following command line
>>
>> gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n
>> paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav
>> test_angle.xvg -b 39000 -e 40000 < test_angle.txt
>>
>> Without the "test_angle.txt" file I need to press the following buttons
>> for selecting the group 0 and 3
>>
>> 0 Enter Ctrl-D 3 Enter Ctrl D.
>>
>> How to include these commands in a text file (e.g.  test_angle.txt)  for
>> that the calculation starts automatically (i.e. for instance with a bash
>> script)
>>
>>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> -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
>
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