[gmx-users] Positive potential energy for TFE solvent
Mark.Abraham at anu.edu.au
Sat Nov 12 00:39:11 CET 2011
On 11/11/2011 5:07 PM, Harpreet Basra wrote:
> I am trying to generate an equilibrated box of 216 TFE molecules.To
> generate the 216 TFE molecule box i performed following steps:
A suggested workflow can be found here
> 1) I got the tfe.gro file and created a cubic box of edge length =
> 0.516 nm containing 1 TFE molecule (at its center), using the
> following command:
>>> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
> I chose this length because in the tfe.gro file dimensions of the TFE
> molecule are 0.516 0.516 0.516.
That's not a good reason. Choose a volume and shape that makes sense for
your target density. Cubic probably doesn't make sense when a
rectangular shape is possible. Then you'll probably want to choose -nbox
> 2) Then using genconf command i replicated the box to get a bigger box
> with 216 TFE molecules using the following command:
>>> genconf -f tfe_box.gro -o out.gro -rot -nbox 6
> 3) Energy minimization was done using STEEPEST descent
> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns
> NPT (300K, 1atm) equilibration.
> After doing all these steps still I obtain a positive a potentail
> energy. I get positive potential energy of the system (2.45+E04
> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive
> total energy of the system. My question is whether obtaining positive
> potential energy indicate some error in my TFE solvent box ? Is it
> because of large Fluorine atoms of TFE ? Does it mean its not properly
> equilibrated ? What can I do to equilibrate it?
You probably have atomic overlaps from your choice of cubic 0.516 box
earlier. Did you look at the results of genconf before computing with them?
More information about the gromacs.org_gmx-users