[gmx-users] Re: Re: Positive potential energy for TFE solvent
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Nov 17 06:48:35 CET 2011
On 16/11/2011 5:02 PM, Harpreet Basra wrote:
> Hi Mark,
> Sorry my last mail was incomplete...here is the complete one!
>
> 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
> distance of 0.5 nm between two adjacent boxes. again the potential is
> positive. here are the results afte genconf and energy minimization:
> Energies (kJ/mol)
> G96Bond G96Angle Proper Dih.
> LJ-14 Coulomb-14
> 2.12101e+02 6.94824e+02 3.88264e-01 6.38056e+01
> 4.67073e+04
> LJ (SR) Coulomb (SR) Coul. recip.
> Potential Pressure (bar)
> -4.10111e+01 -1.68897e+03 -1.39086e+04 3.20399e+04
> -1.31929e+02
> so just after genconf there is no atomic overlap since the molecules
> are far apart,
> the potential is still positive.
Coulomb-14 is far too large. Look at the energy of the pre-miminization
structure too. If you visualize the result of genconf with the periodic
box shown (like I've suggested at least once), then you can start to
address why this intra-molecular contribution is out of control.
Mark
> Thinking of this i tried to visualize the system previously generated
> by me (the one i reported to u earlier). here the system looks
> uniformally distributed with a strong network of hydrogen bonds. I
> confirmed this by calculatein the no. of hydrogen bonds in my
> equilibrated (NVT) trajectory which comes out to be 199 +/- 11.
> moreover the different energy terms from the log file are as follows:
> <==== ############### ==>
> <==== A V E R A G E S ====>
> <== ############### ======>
> Energies (kJ/mol)
> G96Angle Proper Dih. LJ-14 Coulomb-14 LJ
> (SR)
> 2.73173e+03 4.51905e+02 1.90037e+02 4.85110e+04
> -3.35996e+03
> Coulomb (SR) Coul. recip. Potential Kinetic En. Total
> Energy
> -9.37385e+03 -1.52068e+04 2.39441e+04 4.03654e+03
> 2.79807e+04
> Temperature Pressure (bar) Cons. rmsd ()
> 2.99958e+02 2.52412e+02 0.00000e+00
> so do u think that getting a positive total potential energy is a
> result of some atomic overlap or there are actually any repulsive
> forces operative in my TFE solvent system? since even after simple
> genconf when no overlap is possible i get a positive energy.
> Thanks
> Harpreet
>
>
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