[gmx-users] really need some help with g_sas!!

Madhuri Agashe magashe at CLEMSON.EDU
Tue Feb 17 21:40:01 CET 2004


Hi all,
I have a protein fragment which has a chain of 13 residues. I am interested
in finding the changes in solvent accessible area before and after running a
MD run on it. I ran the g_sas command with the -or option. The header for
the xvg output file says @ title "Area per residue", xaxis label "Residue"
and yaxis  label "Area (nm\S2\N)" 

What does the N in the unit stand for?

Also the output in the .xvg file created looks like this:
1	0.276705	0.279141
2	0.361234	0.362187
3	0.330778	0.332667
4	0.25564	0.257268
5	0.398971	0.399676
6	0.373965	0.376628
7	0.465398	0.466495
8	0.27801	0.279602
9	0.235051	0.236743
10	0.16984	0.172215
11	0.149311	0.151239
12	0.0597569	0.0681734
13	0.121558	0.124841
14	0.0709042	0.0762016
15	0.166491	0.171072
16	0.294642	0.298024
17	0.368115	0.368736
18	0.197868	0.200265
19	0.337358	0.338604
	0	4.63489

how do I interpret this? 
Is the first column for time??

Has anyone used g_sas for this before???
Please help!!

Madhuri Agashe





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