On 10/4/12 1:34 AM, Nur Syafiqah Abdul Ghani wrote:
Hi Guys,
Need your help urgently.
I already read a lot of paper about molecular dynamics simulation
which relate work as mine.The main point is to create the mix solvent.
The co-solvent is hexafluoroisopropanol and a lot of researcher cited
the journal name "1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular
dynamics simulations" by Fioroni.
So my question,is the molecule already have a pdb structure?Have
anyone dealing with this compound?
Constructing a coordinate file for a small organic molecule is rather simple
with any number of tools.
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
Because im currently lost due to my HFIP pdb is wrong and the atom
type of F is not recognized and the force field i used is OPLSAA but
right now i think i need to change it to the
GROMOS96..Your advise are highly appreciate..
You should not presume that one force field is inherently better than another
for an arbitrary molecule that is not already parameterized. One could produce
reliable parameters for any force field, provided care is taken to derive and
evaluate them properly.
There seem to be two threads with nearly identical problems. Perhaps you can
cross-reference some information with the other active thread.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
