<div>Hi</div>
<div> </div>
<div> </div>
<div>I am still stuck with same problem of obtaining positive potential energy. </div>
<div> </div>
<div>>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:</div>
<div>>> Hi</div>
<div>>></div>
<div>>> I am trying to generate an equilibrated box of 216 TFE molecules.To</div>
<div>>> generate the 216 TFE molecule box i performed following steps:</div>
<div>> </div>
<div>>A suggested workflow can be found here</div>
<div>><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></div>
<div> </div>
<div>I have been following this link only. </div>
<div> </div>
<div>> </div>
<div>></div>
<div>>> 1) I got the tfe.gro file and created a cubic box of edge length =</div>
<div>>> 0.516 nm containing 1 TFE molecule (at its center), using the</div>
<div>>> following command:</div>
<div>>></div>
<div>>>>> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516</div>
<div>>> I chose this length because in the tfe.gro file dimensions of the TFE</div>
<div>>> molecule are 0.516 0.516 0.516.</div>
<div>> </div>
<div>>That's not a good reason. Choose a volume and shape that makes sense for</div>
<div>>your target density. Cubic probably doesn't make sense when a</div>
<div>>rectangular shape is possible. Then you'll probably want to choose -nbox</div>
<div>>differently later.</div>
<div> </div>
<div>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. </div>
<div> </div>
<div>*****tfe.gro file*****</div>
<div> </div>
<div> <span lang="EN">7
<p>1TFE F1T 1 0.444 0.344 0.246</p>
<p>1TFE CT 2 0.334 0.245 0.246</p>
<p>1TFE F2T 3 0.350 0.160 0.364</p>
<p>1TFE F3T 4 0.350 0.160 0.127</p>
<p>1TFE CH2T 5 0.187 0.326 0.246</p>
<p>1TFE OT 6 0.075 0.220 0.246</p>
<p>1TFE HT 7 -0.019 0.266 0.246</p>
<p>0.49174 0.49174 0.49174</p>
<p> </p>
<p>****topology file****</p><span lang="EN">
<p>[ moleculetype ]</p>
<p>; Name nrexcl</p>
<p>TFE 3</p>
<p>[ atoms ]</p>
<p>; nr type resnr resid atom cgnr charge mass</p>
<p>1 FTFE 1 TFE F1T 1 -0.170 18.9984 </p>
<p>2 CTFE 1 TFE CT 1 0.452 12.0110 </p>
<p>3 FTFE 1 TFE F2T 1 -0.170 18.9984 </p>
<p>4 FTFE 1 TFE F3T 1 -0.170 18.9984 </p>
<p>5 CHTFE 1 TFE CH2T 1 0.273 14.0270 </p>
<p>6 OTFE 1 TFE OT 1 -0.625 15.9994 </p>
<p>7 H 1 TFE HT 1 0.410 1.0080 </p>
<p>[ bonds ]</p>
<p>; ai aj fu c0, c1, ...</p>
<p>2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 </p>
<p>2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 </p>
<p>2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 </p>
<p>2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2 </p>
<p>5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O </p>
<p>6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H </p>
<p>[ pairs ]</p>
<p>; ai aj fu c0, c1, ...</p>
<p>1 6 1 ; F1 O </p>
<p>2 7 1 ; C1 H </p>
<p>3 6 1 ; F2 O </p>
<p>4 6 1 ; F3 O </p>
<p>[ angles ]</p>
<p>; ai aj ak fu c0, c1, ...</p>
<p>1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 </p>
<p>1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 </p>
<p>1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 </p>
<p>3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 </p>
<p>3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 </p>
<p>4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 </p>
<p>2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O </p>
<p>5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H </p>
<p>[ dihedrals ]</p>
<p>; ai aj ak al fu c0, c1, m, ...</p>
<p>6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 </p>
<p>2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H </p></span></span></div>
<div> </div>
<div>and to construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using </div>
<div> </div>
<div> </div>
<div>genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6</div>
<div> </div>
<div> </div>
<div>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. </div>
<div> </div>
<div>thanks</div>
<div> </div>
<div>Harpreet</div>
<div> </div>
<div>> </div>
<div>>> 2) Then using genconf command i replicated the box to get a bigger box</div>
<div>>> with 216 TFE molecules using the following command:</div>
<div>>></div>
<div>>>>> genconf -f tfe_box.gro -o out.gro -rot -nbox 6</div>
<div>>> 3) Energy minimization was done using STEEPEST descent</div>
<div>>></div>
<div>>> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns</div>
<div>>> NPT (300K, 1atm) equilibration.</div>
<div>>></div>
<div>>> After doing all these steps still I obtain a positive a potentail</div>
<div>>> energy. I get positive potential energy of the system (2.45+E04</div>
<div>>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive</div>
<div>>> total energy of the system. My question is whether obtaining positive</div>
<div>>> potential energy indicate some error in my TFE solvent box ? Is it</div>
<div>>> because of large Fluorine atoms of TFE ? Does it mean its not properly</div>
<div>>> equilibrated ? What can I do to equilibrate it?</div>
<div>> </div>
<div>>You probably have atomic overlaps from your choice of cubic 0.516 box</div>
<div>>earlier. Did you look at the results of genconf before computing with them?</div>
<div>> </div>
<div>>Mark</div>
<div> </div>