[gmx-users] Protein Volume

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Thu Jun 5 15:08:01 CEST 2003

> 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.


Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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