On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote:
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.
Did you view the system+box at this stage? What were your actual
commands? You will get much more effective help if you provide an excess
of information, than if you expect people to guess the right follow-up
questions when they have little information.
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.
; RUN CONTROL PARAMETERS
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
; ENERGY MINIMIZATION OPTIONS
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.)
What you've done is fine so far. There is no clear path for these
choices. Ideally you should consider the scheme under which the force
field was parameterized, and how it has been successfully used since,
and do something very similar.
Mark
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.,
IISc, INDIA.
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