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On 16/11/2011 5:02 PM, Harpreet Basra wrote:
<blockquote
cite="mid:CAEAiM5sBhKiS=pF3u9ORVO4CTs5hwSfm9ei1=f9xCSYVhO9HTA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>Hi Mark,</div>
<div> </div>
<div>Sorry my last mail was incomplete...here is the complete
one!</div>
<div> </div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px
0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">On
16/11/2011 1:18 AM, Harpreet Basra wrote:<br>
> Hi Mark,<br>
><br>
> Thanks for the quick reply. But i have already done what
u suggested.<br>
><br>
><br>
><br>
> On 15/11/2011 6:06 PM, Harpreet Basra wrote:<br>
> > Hi<br>
> > I am still stuck with same problem of obtaining
positive potential<br>
> > energy.<br>
> > >>On 11/11/2011 5:07 PM, Harpreet Basra
wrote:<br>
> > >> Hi<br>
> > >><br>
> > >> I am trying to generate an equilibrated
box of 216 TFE<br>
> molecules.To<br>
> > >> generate the 216 TFE molecule box i
performed following steps:<br>
> > ><br>
> > >A suggested workflow can be found here<br>
> > ><a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation</a><br>
> > I have been following this link only.<br>
> > ><br>
> > ><br>
> > >> 1) I got the tfe.gro file and created a
cubic box of edge<br>
> length =<br>
> > >> 0.516 nm containing 1 TFE molecule (at
its center), using the<br>
> > >> following command:<br>
> > >><br>
> > >>>> editconf -f tfe.gro -c -o
tfe_box.gro -bt cubic -box 0.516<br>
> > >> I chose this length because in the
tfe.gro file dimensions<br>
> of the TFE<br>
> > >> molecule are 0.516 0.516 0.516.<br>
> > ><br>
> > >That's not a good reason. Choose a volume
and shape that makes<br>
> sense for<br>
> > >your target density. Cubic probably doesn't
make sense when a<br>
> > >rectangular shape is possible. Then you'll
probably want to<br>
> choose -nbox<br>
> > >differently later.<br>
> > I chose a rectangular box too. still i get a
positive value for<br>
> PE and<br>
> > moreover all the molecules move towards two
opposite walls of<br>
> the box.<br>
> > I am not sure that the way I am using the
genconf command is the<br>
> > correct way. because I have tried every other
possibility for not<br>
> > getting a positive potential, with no success.
So here are my .gro<br>
> > file and the topology file for TFE.<br>
> > *****tfe.gro file*****<br>
> > 7<br>
> ><br>
> > 1TFE F1T 1 0.444 0.344 0.246<br>
> ><br>
> > 1TFE CT 2 0.334 0.245 0.246<br>
> ><br>
> > 1TFE F2T 3 0.350 0.160 0.364<br>
> ><br>
> > 1TFE F3T 4 0.350 0.160 0.127<br>
> ><br>
> > 1TFE CH2T 5 0.187 0.326 0.246<br>
> ><br>
> > 1TFE OT 6 0.075 0.220 0.246<br>
> ><br>
> > 1TFE HT 7 -0.019 0.266 0.246<br>
> ><br>
> > 0.49174 0.49174 0.49174<br>
> ><br>
> > ****topology file****<br>
> ><br>
> > [ moleculetype ]<br>
> ><br>
> > ; Name nrexcl<br>
> ><br>
> > TFE 3<br>
> ><br>
> > [ atoms ]<br>
> ><br>
> > ; nr type resnr resid atom cgnr charge mass<br>
> ><br>
> > 1 FTFE 1 TFE F1T 1 -0.170 18.9984<br>
> ><br>
> > 2 CTFE 1 TFE CT 1 0.452 12.0110<br>
> ><br>
> > 3 FTFE 1 TFE F2T 1 -0.170 18.9984<br>
> ><br>
> > 4 FTFE 1 TFE F3T 1 -0.170 18.9984<br>
> ><br>
> > 5 CHTFE 1 TFE CH2T 1 0.273 14.0270<br>
> ><br>
> > 6 OTFE 1 TFE OT 1 -0.625 15.9994<br>
> ><br>
> > 7 H 1 TFE HT 1 0.410 1.0080<br>
> ><br>
> > [ bonds ]<br>
> ><br>
> > ; ai aj fu c0, c1, ...<br>
> ><br>
> > 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1<br>
> ><br>
> > 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2<br>
> ><br>
> > 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3<br>
> ><br>
> > 2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2<br>
> ><br>
> > 5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O<br>
> ><br>
> > 6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H<br>
> ><br>
> > [ pairs ]<br>
> ><br>
> > ; ai aj fu c0, c1, ...<br>
> ><br>
> > 1 6 1 ; F1 O<br>
> ><br>
> > 2 7 1 ; C1 H<br>
> ><br>
> > 3 6 1 ; F2 O<br>
> ><br>
> > 4 6 1 ; F3 O<br>
> ><br>
> > [ angles ]<br>
> ><br>
> > ; ai aj ak fu c0, c1, ...<br>
> ><br>
> > 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2<br>
> ><br>
> > 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3<br>
> ><br>
> > 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2<br>
> ><br>
> > 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3<br>
> ><br>
> > 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2<br>
> ><br>
> > 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2<br>
> ><br>
> > 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O<br>
> ><br>
> > 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H<br>
> ><br>
> > [ dihedrals ]<br>
> ><br>
> > ; ai aj ak al fu c0, c1, m, ...<br>
> ><br>
> > 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1<br>
> ><br>
> > 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H<br>
> ><br>
> > and to construct a box of TFE solvent i took the
tfe.gro file and<br>
> > replicated the TFE molecule by using<br>
> > genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6<br>
> > can u plz suggest is it that I am using genconf
in a wrong way<br>
> that it<br>
> > is causing this problem? I am not sure how many
molecules (-nbox<br>
> > option in genconf) should i keep in the box in
order to get a mass<br>
> > density of 1383g/L for TFE.<br>
><br>
> That link says "Work out how much volume a single
molecule would<br>
> have in<br>
> the box of your chosen density and size. Useeditconf<br>
> <<a moz-do-not-send="true"
href="http://www.gromacs.org/editconf" target="_blank">http://www.gromacs.org/editconf</a>>to
place a box of that size<br>
> around your<br>
> single molecule." It does not seem to me that you
have done this.<br>
><br>
> Mark<br>
><br>
><br>
> I did place the *single molecule* in a box of size
required to get a<br>
> density of 1383 g/L. I also checked the density of the
solvent box<br>
> (containing 216 molecules after NVT equilibration for 200
ps) I<br>
> constructed the average value comes out to be 1397 g/L
with a std<br>
> deviation of 30 g/L, thus it seems range. Moreover, the
potential<br>
> energy of this one molecule (tfe.gro) was coming out to
be<br>
> highly negative (-6.4E+08 kJ/mol). But on generating a
solvent system<br>
> with 216 TFE molecules the energy becomes (1.9E+04
kJ/mol).<br>
><br>
<br>
Since a single molecule looks OK, the usual reasons for a
large positive<br>
PE would be atomic overlap (visualise the result of genconf -
perhaps a<br>
cubic box is not a good shape), or invalid inter-molecular
non-bonded<br>
parameters (place two boxes 0.5nm apart and see what the
energy does).<br>
<br>
Mark<br>
</blockquote>
<div> </div>
<div>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. <br>
<br>
<br>
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:</div>
<div> </div>
<div>Energies (kJ/mol)<br>
G96Bond G96Angle Proper Dih.
LJ-14 Coulomb-14<br>
2.12101e+02 6.94824e+02 3.88264e-01
6.38056e+01 4.67073e+04<br>
LJ (SR) Coulomb (SR) Coul. recip.
Potential Pressure (bar)<br>
-4.10111e+01 -1.68897e+03 -1.39086e+04 3.20399e+04
-1.31929e+02<br>
</div>
<div>so just after genconf there is no atomic overlap since the
molecules are far apart,</div>
<div>the potential is still positive.</div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEAiM5sBhKiS=pF3u9ORVO4CTs5hwSfm9ei1=f9xCSYVhO9HTA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> </div>
<div>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:</div>
<div> </div>
<div> </div>
<div> <==== ############### ==><br>
<==== A V E R A G E S ====><br>
<== ############### ======> </div>
<div> </div>
<div>Energies (kJ/mol)<br>
G96Angle Proper Dih. LJ-14
Coulomb-14 LJ (SR)<br>
2.73173e+03 4.51905e+02 1.90037e+02 4.85110e+04
-3.35996e+03<br>
Coulomb (SR) Coul. recip. Potential Kinetic En.
Total Energy<br>
-9.37385e+03 -1.52068e+04 2.39441e+04
4.03654e+03 2.79807e+04<br>
Temperature Pressure (bar) Cons. rmsd ()<br>
2.99958e+02 2.52412e+02 0.00000e+00<br>
</div>
<div> </div>
<div>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.</div>
<div> </div>
<div>Thanks </div>
<div>Harpreet</div>
<div> </div>
</div>
<br>
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</blockquote>
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