[gmx-users] SASA: Gromacs5 vs Gromacs4

[morpheus]

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