Abhishek Banerjee wrote:
Hi all,
Actually I want simulate some binary liquid mixture like DMF
and methanol and just want to find diffusion coefficient for each of the
components. But the problem is I am not able to create DMF solvent box.
I have created the .itp and .pdb file of DMF from
http://davapc1.bioch.dundee.ac.uk/prodrg/. I am new to gromacs. If
someone kindly give me some advice, will be helpful for me.
The first thing to know is that you should not necessarily trust the PRODRG
topology at face value. Validate its parameters using methodology compatible
with the force field you intend to use. See here:
http://oldwiki.gromacs.org/index.php/Parameterization
To construct the system, genbox is your friend. Use genbox -ci -nmol -box to
insert the solute into the unit cell, and fill the box with the solvent, also
using genbox. If you need to create a solvent box from which to start, that is
also done with genbox, either using -ci -nmol or -maxsol. The documentation
explains each of these options.
-Justin
Thanking you
abhishek
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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