[gmx-users] question about g_sas

Tom dnaafm at gmail.com
Wed May 6 01:23:34 CEST 2015

Dear GMX developers or users:

What is vdw radius that g_sas uses to calculate the SASA?

Because I tried to change the vdW parameters on ffnonbonded.itp file and
the grompp
to generate a new *tpr file, gmx does not give any change of SASA value.

I checked source code of gmx_sas.c
    /* Get a Van der Waals radius for each atom */
    ndefault = 0;
    for (i = 0; (i < natoms); i++)
        if (!gmx_atomprop_query(aps, epropVDW,

                                *(atoms->atomname[i]), &radius[i]))
        /* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
        radius[i] += solsize;
    if (ndefault > 0)
        fprintf(stderr, "WARNING: could not find a Van der Waals radius for
%d atoms\n", ndefault);


I am wondering if g_sas uses a default database for VdW radius which does
not relate
with LJ parameters on ffnonbond.itp file.

Thanks for the help!


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