From: Nguyen Hoang Phuong <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: [gmx-users] problem with g_sas
Date: Mon, 3 Jul 2006 11:08:12 +0200 (CEST)
Dear All,
I have been using two versions of gromacs to calculate the solvent
accessible surface for one peptide. However, I got totally different
results:
with g_sas (3.1.4)
-------------
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
0 18.1359 14.8618 32.9977 75.6148
2 17.551 14.7032 32.2542 76.3397
4 17.5909 14.9342 32.5251 74.9647
with g_sas (3.3)
-----------
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
0 7.47723 3.36859 10.8458 33.2533
2 7.20544 3.54103 10.7465 32.9583
4 7.23756 3.41761 10.6552 31.1379
I found some new features of g_sas of v. 3.3 over v.3.1.4 as described in
the known bugs section. Is it the reason to make a diference? Or maybe
something else?
Of course, the input files are the same for the two calculations.
The 3.1.4 contained many bugs, which I had fixed for 3.2.
The 3.3 results should be correct.
Berk.
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