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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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