On 11/2/13 6:29 PM, Xu Dong Huang wrote:
Dear All,
My martini system has 3 particles in a chain, rest is martini water, and I’m only
interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I
execute the following:
g_bond -f npt.xtc -n index.ndx -o bonds.xvg
I get the following error:
Total number of samples : 153
Mean : 0.501255
Standard deviation of the distribution: 0.152864
Standard deviation of the mean : 0.0123583
Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1#
-------------------------------------------------------
Program g_bond, VERSION 4.5.5
Source code file: gmx_bond.c, line: 207
Fatal error:
No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Upon inspecting my index files, I see that it defines my 3 particle group as:
[ O1 ]
1 2 3
Then I changed the particle group index file to
[ O1 ]
1 2
2 3
1 3
And I’m still getting the same error.
Any insights?
Use g_dist instead and measure the distances manually. g_analyze can then
produce a distribution of those data.
-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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