[gmx-users] Re: gmx-users Digest, Vol 91, Issue 105
Harpreet Basra
harpreetk.basra at gmail.com
Wed Nov 16 06:34:45 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
>
I tried genconf taking (1) a rectangular box and (2) keeping a distance of
0.5nm between two boxes. What i observe in both the cases is that all the
molecules gather at two opposite walls of the box creating a large empty
space at the center. The reason for this seems to be formation of hydrogen
bonds between the two separate clusters of TFE on both walls. Since on
calculating the hydrogen bonds between the TFEmolecules the average number
comes out to be 189 +/- 34. Also on visualizing the system in VMD i see a
strong network of hydrogen bonds in the two separated clusters.
Apart from this u asked me to see the result after genconf. So i calculated
the energies just after genconf for the system having a
Thinking of this I tried to see how my generated system looks in the
previous case (which i reported to u in last mail). I see (in VMD) that now
the system looks uniformally distributed and
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