[gmx-users] DOPC lipid bilayer
tsjerkw at gmail.com
Mon Apr 23 11:39:49 CEST 2007
On 4/23/07, naga raju <nagaraju_cy at yahoo.co.in> wrote:
> Dear gmx users,
> I am thankful to Tsjerk Wassenaar and Chris
> Neale, to their suggestions. I prepared dopc.itp parameter file for DOPC
> lipid bilayer. To Protein+DOPC bilayer system, which force field I have to
> choose to my protein.
That is up to you and should be chosen based on certain criteria you
or the field sets. E.g. do you want all atoms or united atoms? What
has been used previously on that system? In any case, the force field
used for the lipids should match the one used for the protein. If
you've parameterized the thing for a gromos force field, use that
gromos force field. And please don't let it be ffgmx... In case it is,
check the archives for reasons not to use that force field (or note
the word 'deprecated' pdb2gmx gives you).
On another note, don't include a whole days digest in your mail when
you reply! Please only include relevant parts. (Mark will probably
note that a while ago I gave the same remark, while automatically
including the digest again..., which I herewith want to set right ;)).
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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