[gmx-users] syntax for gmx distance

[Justin Lemkul]

On 9/14/15 7:08 AM, Nash, Anthony wrote:
> 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

Nope.

> I want to do is measure the distance between the COM of two groups defined
> in an index file.
>

And what you're doing is, in principle, correct.  I have no explanation for why 
you're getting an error, unless there's some weird mismatch with the index 
(capitalization?) or something else going on.  The first selection fails, so 
naturally anything after "plus" will fail as being invalid.

-Justin

> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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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

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