[gmx-users] Fwd: Obtaining Positive Energy Values for Both Potential and Total Energies

[Mark Abraham]

Hi,

Please leave the discussion on the list. Others may wish to contribute or
learn from it! :-)

---------- Forwarded message ----------
From: Yip Yew Mun <yipy0005 at gmail.com>
Date: Thu, Jul 24, 2014 at 5:16 AM
Subject: Re: [gmx-users] Obtaining Positive Energy Values for Both
Potential and Total Energies
To: mark.j.abraham at gmail.com


Hi Mark,

Thanks for the prompt reply. I have been trying to obtain the water/octanol
partition coefficient of a certain small molecule in TI simulations, in
which the result would be compared to the experimental value. That’s the
reason why I’m attempting simulations with octanol as the solvent. I have
tried topologies from users-contributed gromacs topologies (
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
<http://www.gromacs.org/index.php?title=Download_&_Installation/User_contributions/Molecule_topologies>)
as well as from VirtualChemistry. However, since they are described to be
equilibrated already, I simply tried to re-run the equilibration to verify
it myself. But when I did it, the potential energy values are positive.
Therefore, I wish to ask if you know of any sites or in your opinion how
should I equilibrate a non-water solvent?


It's not fundamentally any different (but see
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation for some
clues). If the energies are positive, then either your methodology was
wrong (does it work for a water box? for DMSO or something?), or the model
is wrong (which is why I suggested the things I already suggested).

Mark