On 2/14/14, 6:55 AM, jhosamelly wrote:
Hi! Follow up question on this.
I'm getting the xvg file i want but the interval is .5.
This is too big for me since I want to get the bilayer thickness.
Bilayer thickness from g_density is probably not very accurate.
what additional options should I add to
g_density -f confout.gro -n index.ndx -o martini.xvg
to get a better xvg output file.
You can tune the thickness of each slice by setting how many slices there are
with -sl.
-Justin
BTW, I increased the box size along the Z to have some vacuum on the system.
when I haven't done this I got.
0 0
0.131134 21.208
0.262267 42.416
0.393401 42.416
0.524534 169.664
0.655668 381.744
0.786802 360.536
0.917935 212.08
1.04907 190.872
1.1802 42.416
1.31134 0
1.44247 0
1.5736 0
1.70474 0
1.83587 0
1.967 0
2.09814 0
2.22927 0
2.3604 0
2.49154 0
2.62267 0
2.75381 0
2.88494 0
3.01607 0
3.14721 0
3.27834 0
3.40947 0
3.54061 0
3.67174 0
3.80287 0
3.93401 0
4.06514 0
4.19628 0
4.32741 0
4.45854 0
4.58968 0
4.72081 0
4.85194 63.624
4.98308 127.248
5.11421 296.912
5.24534 318.12
5.37648 339.328
5.50761 84.832
5.63874 21.208
5.76988 0
5.90101 0
6.03215 0
6.16328 0
6.29441 0
6.42555 0
density for P*.
then when I increased the box size along the z the density output for P*
became
0 0
0.5 0
1 0
1.5 0
2 0
2.5 0
3 0
3.5 0
4 0
4.5 0
5 0
5.5 0
6 0
6.5 0
7 0
7.5 0
8 0
8.5 0
9 5.56217
9.5 150.178
10 228.049
10.5 0
11 0
11.5 0
12 0
12.5 0
13 0
13.5 0
14 139.054
14.5 189.114
15 0
15.5 0
16 0
16.5 0
17 0
17.5 0
18 0
18.5 0
19 0
19.5 0
20 0
20.5 0
21 0
21.5 0
22 0
22.5 0
23 0
23.5 0
24 0
24.5 0
Thanks guys! :)
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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
http://mackerell.umaryland.edu/~jalemkul
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