[gmx-users] Protein Volume

[Pedro Alexandre Lapido Loureiro]

> Hello,
> 
> is it possible to calculate the protein volume with GROMACS? How?
> 
> Thanks in advance,
> 
> Leonardo De Maria, Ph.D.
> Research Scientist
> Novozymes A/S
> Smørmosevej 25
> 2880 Bagsværd
> Denmark
> 
> Phone:  +45 44421890
> Fax:      +45 44980246
> 
> e.mail: ledm at novozymes.com
> 
> 
> 
You may calculate the specific volume.
Run a simulation of your water model in the same conditions.
Measure the box volume (g_energy) and find the volume per water molecule.
Now measure the box volume of your protein+water simulation.
As long as you know the number of water molecules in your system, you will 
find the protein specific volume.

Regards,
Pedro.

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil