[gmx-users] SASA: Gromacs5 vs Gromacs4
morpheus
morpheus.sommer2008 at gmail.com
Mon Nov 16 16:18:05 CET 2015
Hi
I'm having some trouble in reproducing SASA values of Gromacs 4 with
Gromacs 5. Instead of giving the surface and output group via the command
line I have tried to use the -surface and -output option but the results
differ. The difference is not huge but still there. Any idea what I am
doing wrong (see 2 examples below)?
Thanks!
Morpheus
####### example 1
# This file was created Mon Nov 16 14:54:18 2015
# Created by:
# GROMACS: gmx sasa, VERSION 5.0.6
# Executable: /bin/gmx
# Library dir: /usr/share/gromacs/top
# Command line:
# gmx sasa -f 1G4.final.md.xtc -s 1G4.md.tpr -n 1G4.ndx -o
peptideTestSASA.g1_g13.xvg -dt 80 -surface 1 -output 20
# gmx is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Total"
@ s1 legend "chC"
0.000 287.071 0.568
2000.000 306.356 1.917
4000.000 302.343 2.007
6000.000 305.080 1.359
8000.000 299.480 1.711
10000.000 297.861 1.306
# This file was created Fri Jun 12 11:09:38 2015
# by the following command:
# g_sas -f 1G4.final.md.xtc -s 1G4.md.tpr -n 1G4.ndx -o
1G4.sasa.peptide.xvg -dt 80
#
# g_sas is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
0 0.957754 0.897288 1.85504 5.80438
2000 1.81419 1.58177 3.39596 12.503
4000 1.71511 1.60255 3.31766 10.9263
6000 1.34735 1.34146 2.68881 7.51391
8000 1.80347 1.25413 3.0576 10.153
10000 1.18446 1.3283 2.51276 8.38755
##### example 2
# This file was created Mon Nov 16 15:01:43 2015
# Created by:
# GROMACS: gmx sasa, VERSION 5.0.6
# Executable: /bin/gmx
# Library dir: /usr/share/gromacs/top
# Command line:
# gmx sasa -f 1A.final.md.xtc -s 1A.md.tpr -n 1A.ndx -o
1A.sasa.peptide_v5.xvg -surface 1 -output 13
# gmx is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Total"
@ s1 legend "chC"
0.000 200.554 2.674
125.000 212.356 2.591
250.000 212.251 2.665
375.000 214.800 2.616
500.000 216.103 2.642
# This file was created Wed Jan 29 14:24:11 2014
# by the following command:
# g_sas -f 1A.final.md.xtc -s 1A.md.tpr -n 1A.ndx -o 1A.sasa.peptide.xvg
#
# g_sas is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
0 2.11366 1.816 3.92966 13.3406
125 2.17524 1.36085 3.53609 13.324
250 2.14445 1.45416 3.59862 13.0897
375 2.34261 1.57459 3.91719 13.5379
500 2.29662 1.74904 4.04566 13.3061
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