aiswarya pawar wrote:
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000000 0.6259024 0.3880000 0.3610001 -0.3329997
1.0000000 0.6778775 0.2590003 0.5939999 -0.1989999
2.0000000 0.6759030 0.2529998 0.5939999 -0.2000003
3.0000000 0.6463353 0.1690001 0.5680003 -0.2579999
4.0000000 0.6808891 0.2639999 0.6050000 -0.1669998
5.0000000 0.6883561 0.3090000 0.5920000 -0.1670003
6.0000000 0.6201660 0.2769997 0.5139999 -0.2090001
7.0000000 0.6832005 0.2910001 0.5809999 -0.2110000
8.0000000 0.6472999 0.2960002 0.5339999 -0.2150002
9.0000000 0.6542692 0.1880000 0.5400000 -0.3180003
10.0000000 0.6725602 0.3230002 0.5780001 -0.1180000
11.0000000 0.6138712 0.3470001 0.4769998 -0.1700001
12.0000000 0.6999645 0.2860000 0.6150002 -0.1729999
13.0000000 0.6504593 0.1200001 0.6160002 -0.1710000
14.0000000 0.6447160 0.2110000 0.5869999 -0.1629996
15.0000000 0.6645610 0.2040000 0.5710001 -0.2720003
16.0000000 0.6481276 0.2330003 0.5560002 -0.2379999
17.0000000 0.6511113 0.2240002 0.5609999 -0.2430000
18.0000000 0.7119258 0.2650001 0.6220002 -0.2230000
19.0000000 0.6653563 0.0929999 0.6170001 -0.2309999
20.0000000 0.6881638 0.2520001 0.6070004 -0.2040000
21.0000000 0.7161944 0.2090001 0.6220002 -0.2870002
22.0000000 0.6587778 0.1400001 0.6020002 -0.2279997
23.0000000 0.5798631 0.0170002 0.5160003 -0.2639999
24.0000000 0.5862564 0.0390000 0.5239997 -0.2599998
25.0000000 0.6923014 -0.1240001 0.5520000 -0.3990002
26.0000000 0.5787479 -0.0899997 0.5050001 -0.2680001
27.0000000 0.5776323 -0.2589998 0.4730000 -0.2070003
28.0000000 0.5910018 -0.1630001 0.5250001 -0.2170000
29.0000000 0.4448786 -0.1570001 0.4020000 -0.1079998
30.0000000 0.4806164 -0.2160001 0.4000001 -0.1560001
31.0000000 0.5405830 -0.1700001 0.4730000 -0.1989999
32.0000000 0.5614526 -0.1080003 0.4930000 -0.2459998
33.0000000 0.4994450 -0.0730000 0.4500003 -0.2040000
34.0000000 0.5323368 -0.1420002 0.4830003 -0.1730003
From this the first column is the time and the second is the water
protein atom distance. so when am using the g_analyze i would use the
1st and 2nd column for the input? More over now this distances are below
Pass this file directly to g_analyze - there's no need for manipulation. You'll
get averages of all four distance columns, but of course just take what you need.
0.8 nm . what would i do if my data in between shows distance more than
0.8nm.
You said you had g_dist measure distances between protein atoms and the COM of
water molecules within 0.8 nm, so I don't see how a distance greater than 0.8 nm
is even possible in this case.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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