[gmx-users] syntax for gmx distance

[Nash, Anthony]

Thanks Justin,

Turns out the cluster has versions 4.5.5, and 5 to 5.0.6. Doesn’t work on
any of the 5’s. I don’t have access to 5.1 yet. What’s more, I have no
idea why only half the tools for 4.5.5 are missing on this cluster,
including grommp so I can’t recompile a .tpr. Any suggestions on to shift
between versions with my trajectory, as g_dist won’t work given my current
.tpr file (5.0.5). 

Totally understand that this is somewhat of an arcane approach, and that
pushing for the latest and greatest version is always best. I was just
hoping to double check my umbrella sampling data points were over lapping
in all 3 dimensions given that I am using an absolute distance reaction
coordinate. 

Thanks
Anthony 

Dr Anthony Nash
Department of Chemistry
University College London





On 14/09/2015 12:12, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
>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
>
>==================================================
>-- 
>Gromacs Users mailing list
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