Hi Mark, Thanks for the quick reply. But i have already done what u suggested.
> > On 15/11/2011 6:06 PM, Harpreet Basra wrote: > > 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. > > That link says "Work out how much volume a single molecule would have in > the box of your chosen density and size. Useeditconf > <http://www.gromacs.org/editconf>to place a box of that size around your > single molecule." It does not seem to me that you have done this. > > Mark > I did place the *single molecule* 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). Harpreet
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