Hi Mark,<div><br></div><div>Thanks for the quick reply. But i have already done what u suggested.<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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 molecules.To<br>
> >> generate the 216 TFE molecule box i performed following steps:<br>
> ><br>
> >A suggested workflow can be found here<br>
> ><a 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 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 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 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 choose -nbox<br>
> >differently later.<br>
> I chose a rectangular box too. still i get a positive value for PE and<br>
> moreover all the molecules move towards two opposite walls of 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 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 have in<br>
the box of your chosen density and size. Useeditconf<br>
<<a href="http://www.gromacs.org/editconf" target="_blank">http://www.gromacs.org/editconf</a>>to place a box of that size around your<br>
single molecule." It does not seem to me that you have done this.<br>
<br>
Mark<br></blockquote><div><br></div>I did place the <b>single molecule</b> 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). </div>
</div><div class="gmail_quote"><br></div><div class="gmail_quote">Harpreet</div>