[gmx-users] NVT equilibration of ethanol in OPLSAA ff

Ravi Kumar Venkatraman ravikumarvenkatraman at gmail.com
Wed Oct 5 09:36:56 CEST 2011

Dear All,
             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.

integrator               = steep
; start time and timestep in ps
tinit                    = 0
dt                       = 0.001
nsteps                   = 10000
nstlist                  = 10
rlist                    = 1.1
coulombtype              = pme
pme_order                = 4
fourierspacing           = 0.16
rcoulomb                 = 1.1
vdw-type                 = cut-off
rvdw                     = 1.1
nstenergy                = 10
emtol                    = 1000.0
emstep                   = 0.1

I saw the em.xvg file it is minimized well.
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.

Thank you.

With Regards,
Ravi Kumar Venkatraman,
IPC Dept.,
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