[gmx-users] Re: Positive potential energy for TFE solvent
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 15 15:33:55 CET 2011
On 16/11/2011 1:18 AM, Harpreet Basra wrote:
> Hi Mark,
>
> Thanks for the quick reply. But i have already done what u suggested.
>
>
>
> 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
>
>
> I did place the *single molecule* in a box of size required to get a
> density of 1383 g/L. I also checked the density of the solvent box
> (containing 216 molecules after NVT equilibration for 200 ps) I
> constructed the average value comes out to be 1397 g/L with a std
> deviation of 30 g/L, thus it seems range. Moreover, the potential
> energy of this one molecule (tfe.gro) was coming out to be
> highly negative (-6.4E+08 kJ/mol). But on generating a solvent system
> with 216 TFE molecules the energy becomes (1.9E+04 kJ/mol).
>
Since a single molecule looks OK, the usual reasons for a large positive
PE would be atomic overlap (visualise the result of genconf - perhaps a
cubic box is not a good shape), or invalid inter-molecular non-bonded
parameters (place two boxes 0.5nm apart and see what the energy does).
Mark
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