[gmx-users] Positive potential energy for TFE solvent

Tue Nov 15 08:21:10 CET 2011

On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> Hi
> I am still stuck with same problem of obtaining positive potential 
> energy.
> >>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
> I have been following this link only.
> >
> >
> >> 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.
> I chose a rectangular box too. still i get a positive value for PE and 
> moreover all the molecules move towards two opposite walls of the box. 
> I am not sure that the way I am using the genconf command is the 
> correct way. because I have tried every other possibility for not 
> getting a positive potential, with no success. So here are my .gro 
> file and the topology file for TFE.
> *****tfe.gro file*****
> 7
>
> 1TFE   F1T   1   0.444   0.344   0.246
>
> 1TFE   CT     2   0.334  0.245   0.246
>
> 1TFE   F2T    3   0.350  0.160   0.364
>
> 1TFE   F3T    4   0.350  0.160   0.127
>
> 1TFE   CH2T  5  0.187  0.326   0.246
>
> 1TFE   OT      6  0.075  0.220   0.246
>
> 1TFE   HT      7  -0.019 0.266   0.246
>
> 0.49174   0.49174   0.49174
>
> ****topology file****
>
> [ moleculetype ]
>
> ; Name nrexcl
>
> TFE 3
>
> [ atoms ]
>
> ; nr type resnr resid atom cgnr charge mass
>
> 1 FTFE    1  TFE  F1T   1   -0.170   18.9984
>
> 2 CTFE    1  TFE  CT    1    0.452   12.0110
>
> 3 FTFE    1  TFE  F2T   1   -0.170   18.9984
>
> 4 FTFE    1  TFE  F3T   1   -0.170   18.9984
>
> 5 CHTFE 1  TFE  CH2T 1    0.273   14.0270
>
> 6 OTFE   1  TFE  OT     1   -0.625   15.9994
>
> 7 H          1  TFE  HT     1   0.410   1.0080
>
> [ bonds ]
>
> ; ai aj fu c0, c1, ...
>
> 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1
>
> 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2
>
> 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3
>
> 2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2
>
> 5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O
>
> 6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H
>
> [ pairs ]
>
> ; ai aj fu c0, c1, ...
>
> 1 6 1 ; F1 O
>
> 2 7 1 ; C1 H
>
> 3 6 1 ; F2 O
>
> 4 6 1 ; F3 O
>
> [ angles ]
>
> ; ai aj ak fu c0, c1, ...
>
> 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2
>
> 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3
>
> 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2
>
> 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3
>
> 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2
>
> 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2
>
> 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O
>
> 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H
>
> [ dihedrals ]
>
> ; ai aj ak al fu c0, c1, m, ...
>
> 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1
>
> 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H
>
> and to construct a box of TFE solvent i took the tfe.gro file and 
> replicated the TFE molecule by using
> genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6
> can u plz suggest is it that I am using genconf in a wrong way that it 
> is causing this problem? I am not sure how many molecules (-nbox 
> option in genconf) should i keep in the box in order to get a mass 
> density of 1383g/L for TFE.

That link says "Work out how much volume a single molecule would have in 
the box of your chosen density and size. Useeditconf 
<http://www.gromacs.org/editconf>to place a box of that size around your 
single molecule." It does not seem to me that you have done this.

Mark

> thanks
> Harpreet
> >
> >> 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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