On 11/11/2011 5:07 PM, Harpreet Basra wrote:
Hi
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
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
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
differently later.
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?
Mark
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