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. thanks Harpreet > >> 2) Then using genconf command i replicated the box to get a bigger box >> with 216 TFE molecules using the following command: >> >>>> genconf -f tfe_box.gro -o out.gro -rot -nbox 6 >> 3) Energy minimization was done using STEEPEST descent >> >> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns >> NPT (300K, 1atm) equilibration. >> >> After doing all these steps still I obtain a positive a potentail >> energy. I get positive potential energy of the system (2.45+E04 >> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive >> total energy of the system. My question is whether obtaining positive >> potential energy indicate some error in my TFE solvent box ? Is it >> because of large Fluorine atoms of TFE ? Does it mean its not properly >> equilibrated ? What can I do to equilibrate it? > >You probably have atomic overlaps from your choice of cubic 0.516 box >earlier. Did you look at the results of genconf before computing with them? > >Mark
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
