[gmx-users] g_rotacf error

Justin Lemkul jalemkul at vt.edu
Wed Oct 30 02:33:56 CET 2013

On 10/29/13 4:02 PM, Tiago Gomes wrote:
> Hello gromacs users,
> I´m currently tring to calculate S2 order parameters for comparison with
> nmr data and other simulations.
> When i try the command for the NH vector:
> g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w
> -noaver
> It gives me the only half of the residues (NH vectors). It detects the
> index file with the correct number of atoms, but i only get data for 57
> residues.
>>From the log: Group     0 (             NH) has   114 elements
> Tried a lot o playing with the index file to no sucess. The conversion of
> the tpr file to a pdb seems to give the correct numbering. Any insights?

Having never used g_rotacf, I can only offer a guess.  If you have 114 elements 
in the index file (an N and an H for each residue, presumably), then that indeed 
corresponds to 57 residues.  Oddly, though, this should not be how g_rotacf 
works.  According to the help description, the index group should be composed of 
atom triplets.  The fact that 114 is evenly divisible by 3 is probably why the 
command doesn't crash outright.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list