Dear All,<br> I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I scaled the solvent box for the density of ethanol (785.22 g/l) at 298.15. Before creatin solvent box I EM the isolated solvent molecule, then I used that molecule to generate the solvent box. Then I EM the solvent box 512 molecules.Followin are the parameters for EM of Solvent box.<br>
<br>; RUN CONTROL PARAMETERS<br>integrator = steep<br>; start time and timestep in ps<br>tinit = 0<br>dt = 0.001<br>nsteps = 10000<br>nstlist = 10<br>
rlist = 1.1<br>coulombtype = pme<br>pme_order = 4<br>fourierspacing = 0.16<br>rcoulomb = 1.1<br>vdw-type = cut-off<br>rvdw = 1.1<br>
nstenergy = 10<br>; ENERGY MINIMIZATION OPTIONS<br>emtol = 1000.0<br>emstep = 0.1<br> <br>I saw the em.xvg file it is minimized well.<br>Then I started NVT equilibration with lincs constraints for hbonds at timesteps of 0.2 fs and runned for 5 ps. The resultant configuration shows that most of the molecules were together at region of box and there was some void inside the box. I used cut-off of 1.1 nm for electrostatic and VdW interactions. I didn't use any shift or switch function. (can anybody suggest me a good tutorial to understand the judicious use of this functions.) Please help me sort this problem. If you need further details I am ready to send you.<br>
<br>Thank you.<br><br>With Regards,<br>Ravi Kumar Venkatraman,<br>IPC Dept.,<br>IISc, INDIA.<br><br><br><br>