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On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote:
<blockquote
cite="mid:CA+c-nQxUeCRVQ=t80PTvn0q7Jrjnep-49qmHAzfEy9XGf5K5XA@mail.gmail.com"
type="cite">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.</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CA+c-nQxUeCRVQ=t80PTvn0q7Jrjnep-49qmHAzfEy9XGf5K5XA@mail.gmail.com"
type="cite"> 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.)</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+c-nQxUeCRVQ=t80PTvn0q7Jrjnep-49qmHAzfEy9XGf5K5XA@mail.gmail.com"
type="cite"> 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>
<br>
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<br>
</blockquote>
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