[gmx-users] SASA: Gromacs5 vs Gromacs4

[Justin Lemkul]

On 11/16/15 10:18 AM, morpheus wrote:
> 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)?
>

There were changes to vdwradii.dat to use better-sourced values. The screen 
output should have a prominent warning about this fact and that results will change.

-Justin

> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================