[gmx-users] syntax for gmx distance

[Nash, Anthony]

Hi Justin,

Yep, it is 5.0.5 installed on the cluster. I¹d have to install a new
version of gromacs somewhere else if I can. In the meanwhile, is there
anyway to call the old g_dist on a 5.0.5 release (I am guessing not). All
I want to do is measure the distance between the COM of two groups defined
in an index file. 

Thanks
Anthony





On 14/09/2015 11:57, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
>On 9/14/15 6:29 AM, Nash, Anthony wrote:
>> Just downloaded the .tpr and .trr to my machine and tried exactly the
>>same
>> command:
>> 
>> gmx distance -n index.ndx -f umb_1_all.trr -s umb_1_umb.tpr -oh
>> umb_1_distance_hist.xvg -oall umb_1_distance.xvg -select 'com of group
>> "ZINC" plus com of group "CARBONYL"'
>> 
>> It spits out the same error:
>> 
>> Invalid command-line options
>>      In command-line option -select
>>        In keyword 'com'
>>          required parameter 'of' not specified
>>        invalid selection 'com'
>>      In command-line option -select
>>        syntax error
>>        invalid selection 'group'
>>      In command-line option -select
>>        syntax error
>>        invalid selection 'plus'
>>      In command-line option -select
>>        In keyword 'com'
>>          required parameter 'of' not specified
>>        invalid selection 'com'
>>      In command-line option -select
>>        syntax error
>>        invalid selection 'group'
>> 
>
>I can't reproduce the problem with the latest development version;
>everything
>works fine.  Can you try with version 5.1?  I'm assuming you're using
>5.0.5
>based on the naming of the script in the previous message.
>
>-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
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>
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