[gmx-users] syntax for gmx distance

[Nash, Anthony]

Hi Justin,

Gmx distance, grompp, etc… all execute fine. The "$CHEM/rungromacs505” is
how gromacs is executed on this particular cluster I am using (different,
from say, using a more traditional “module load gromacs..” approach).

Thanks
Anthony 


On 14/09/2015 11:18, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
>On 9/14/15 4:28 AM, Nash, Anthony wrote:
>> Dear all,
>>
>>
>> I understand that this is quite a basic question, but I think I need a
>> fresh set of eyes to figure out what¹s going on with gmx distance
>>-select
>> syntax.
>>
>> In my index file, I have 23 groups, two of which are ³ZINC² and
>>³CARBONYL²
>>
>> Based on numerous mail archive suggestions and the gromacs website
>>change
>> in tools page, I¹m using:
>>
>> $CHEM/rungromacs505 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"'
>>
>>
>> Which kicks up the 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'
>>
>> I¹d appreciate any suggestions. I¹ve also tried to do *something* via
>>the
>> interactive command line (when -select is not supplied), but what it¹s
>> asking for is a bit cryptic.
>>
>
>What is $CHEM/rungromacs505?  I suspect that's your problem.
>
>-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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