On 11/2/13 7:01 PM, Xu Dong Huang wrote:
Should I perhaps make an edit in the index file for group 1 to be particle 1
and 2, and group 2 = particle 2 and 3?
No. If you want three different distances, you need three groups, as I said in
my previous message, and I even wrote the exact index file for you.
-Justin
On Nov 2, 2013, at 6:50 PM, Xu Dong Huang <xudonghm...@gmail.com> wrote:
@ Gromacs users,
so I did g_dist , and I’m confused by a couple of things. 1) why is it asking
me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1
2 3, and nothing else. 2) I just picked the same group twice, and the
result is gives me in xvg is the following
There are no distances measured, that cannot be right.
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
20.0000000 0.0000000 0.0000000 0.0000000 0.0000000
40.0000000 0.0000000 0.0000000 0.0000000 0.0000000
60.0000000 0.0000000 0.0000000 0.0000000 0.0000000
80.0000000 0.0000000 0.0000000 0.0000000 0.0000000
100.0000000 0.0000000 0.0000000 0.0000000 0.0000000
120.0000000 0.0000000 0.0000000 0.0000000 0.0000000
140.0000000 0.0000000 0.0000000 0.0000000 0.0000000
160.0000000 0.0000000 0.0000000 0.0000000 0.0000000
180.0000000 0.0000000 0.0000000 0.0000000 0.0000000
200.0000000 0.0000000 0.0000000 0.0000000 0.0000000
220.0000000 0.0000000 0.0000000 0.0000000 0.0000000
240.0000000 0.0000000 0.0000000 0.0000000 0.0000000
260.0000000 0.0000000 0.0000000 0.0000000 0.0000000
…
Thanks in advance,
Xu Huang
On Nov 2, 2013, at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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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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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