Hello,
I am using the Gromacs 4.6.5 g_sas tool with custom radii for each atom as
specified with a local vdwradii.dat file.
Are the surface areas reported in -or atomarea.xvg on a sphere defined by
R_VDW or at R_VDW + R_probe?
Similarly, is the -minarea # flag a threshold value that applies to
On Mon, Jan 19, 2015 at 12:39 AM, Christopher Neale
chris.ne...@alum.utoronto.ca wrote:
Dear Users:
I presume that I can use tabulated non-bonded potentials with replica
exchange in gromacs 4.6.7.
Indeed, I can think of no reason why not (modulo that there's only support
for those in the
Dear GROMACS users and developers,
In GMX 4.6 or up, 'mdrun' can automatically adjust direct and
reciprocal part of PME calculation to boost up speed. But how does it
actually implemented in the code? I tried to manually set PME cutoff
and fourierspacing but get different result. Can
Hi Pratibha
If you make the index file with only the backbone atoms the dangle.trr file
generated from
g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral
Gives you only the sine and cosine of backbone phi and psi dihedral angles
. You can check for it by converting your
Dear GROMACS developers,
In GMX 4.6 or up, 'mdrun' can automatically adjust direct and
reciprocal part of PME calculation to boost up speed. But how does it
actually implemented in the code? I tried to manually set PME cutoff
and fourierspacing but get different result. Can someone explain
Dear GROMACS users and developers,
In GMX 4.6 or up, 'mdrun' can automatically adjust direct and
reciprocal part of PME calculation to boost up speed. But how does it
actually implemented in the code? I tried to manually set PME cutoff
and fourierspacing but get different result. Can
Dear GROMACS developers,
In GMX 4.6 or up, 'mdrun' can automatically adjust direct and
reciprocal part of PME calculation to boost up speed. But how does it
actually implemented in the code? I tried to manually set PME cutoff
and fourierspacing but get different result. Can someone explain
Dear GROMACS users and developers,
In GMX 4.6 or up, 'mdrun' can automatically adjust direct and
reciprocal part of PME calculation to boost up speed. But how does it
actually implemented in the code? I tried to manually set PME cutoff
and fourierspacing but get different result. Can
On Thu, Jan 15, 2015 at 3:21 AM, Jiaqi Lin jq...@mit.edu wrote:
Dear GMX developers,
I've encounter a problem in GROMACS concerning the auto-tuning feature of
PME that bugged me for months. As stated in the title, the auto-tuning
feature of mdrun changed my coulomb cutoff from 1.4 nm to ~3.3
