<div>hi,</div>
<div> </div>
<div>I am still stuck with same problem of obtaining positive potential energy. <br> <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>
<br>I have been following this link only. <br> <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> <br>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><br> the energy of this one molecule (tfe.gro) was coming out to b e highly negative (-6.4E+08 kJ/mol). But on generating a solvent system with 216 molecules the energy becomes (1.9E+04 kJ/mol). </div>
<div><br>******tfe.gro file*****<br> <br> 7 <br>1TFE F1T 1 0.444 0.344 0.246<br>1TFE CT 2 0.334 0.245 0.246<br>1TFE F2T 3 0.350 0.160 0.364<br>1TFE F3T 4 0.350 0.160 0.127<br>1TFE CH2T 5 0.187 0.326 0.246<br>
1TFE OT 6 0.075 0.220 0.246<br>1TFE HT 7 -0.019 0.266 0.246<br>0.49174 0.49174 0.49174<br> <br>****topology file****<br>[ moleculetype ]<br>; Name nrexcl<br>TFE 3<br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br>
1 FTFE 1 TFE F1T 1 -0.170 18.9984 <br>2 CTFE 1 TFE CT 1 0.452 12.0110 <br>3 FTFE 1 TFE F2T 1 -0.170 18.9984 <br>4 FTFE 1 TFE F3T 1 -0.170 18.9984 <br>5 CHTFE 1 TFE CH2T 1 0.273 14.0270 <br>
6 OTFE 1 TFE OT 1 -0.625 15.9994 <br>7 H 1 TFE HT 1 0.410 1.0080 <br>[ bonds ]<br>; ai aj fu c0, c1, ...<br>2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 <br>2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 <br>
2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 <br>2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2 <br>5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O <br>6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H <br>[ pairs ]<br>; ai aj fu c0, c1, ...<br>
1 6 1 ; F1 O <br>2 7 1 ; C1 H <br>3 6 1 ; F2 O <br>4 6 1 ; F3 O <br>[ angles ]<br>; ai aj ak fu c0, c1, ...<br>1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 <br>1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 <br>1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 <br>
3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 <br>3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 <br>4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 <br>2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O <br>5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H <br>
[ dihedrals ]<br>; ai aj ak al fu c0, c1, m, ...<br>6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 <br>2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H <br> <br>To construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using <br>
<br> <br>genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6<br> <br> <br>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. Though i checked the denity of solvent box i constructed the average valu comes out to be 1397g/L with a std deviation of 30g/L. thus it seems range.<br>
<br>thanks<br> <br>Harpreet<br> <br>> <br>>> 2) Then using genconf command i replicated the box to get a bigger box<br>>> with 216 TFE molecules using the following command:<br>>><br>>>>> genconf -f tfe_box.gro -o out.gro -rot -nbox 6<br>
>> 3) Energy minimization was done using STEEPEST descent<br>>><br>>> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns<br>>> NPT (300K, 1atm) equilibration.<br>>><br>>> After doing all these steps still I obtain a positive a potentail<br>
>> energy. I get positive potential energy of the system (2.45+E04<br>>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive<br>>> total energy of the system. My question is whether obtaining positive<br>
>> potential energy indicate some error in my TFE solvent box ? Is it<br>>> because of large Fluorine atoms of TFE ? Does it mean its not properly<br>>> equilibrated ? What can I do to equilibrate it?<br>
> <br>>You probably have atomic overlaps from your choice of cubic 0.516 box<br>>earlier. Did you look at the results of genconf before computing with them?<br>> <br>>Mark</div>