AMBER Archive (2003)

Subject: Re: Lipids

From: Arvid Soederhaell (arvid_at_fmp-berlin.de)
Date: Tue Mar 18 2003 - 04:33:15 CST

Hi Gemma
I have developed a DPPC lipid model using the Cornell-95 f.f.. The model
works relatively OK, but some things are not that good. For example the
area/lipid is slightly too small and the order parameters are slightly too
high (in the liquid chrystaline phase). The system is stable using sander
from AMBER7, but not sander in AMBER6 (don't ask me why). Ewald
summation (PME) seems to be important for these systems, at least using
amber and Mdynamix (see Soederhaell Laaksonen, J. Phys. Chem. B 2001, 105
9308-).
While I have had some problem in tuning the model in amber, i have started
to test if gromacs can do this better. So far i have no results, but given
the number of publications concerning lipid simulaitons that uses gromacs
compared to amber, it is tempting to believe that gromacs is better for
these systems.

It would be very useful for me if you could share your own experiences on
this topic, because i would like to be able to use amber for lipid
simulations because of other technical reasons.

Let me know if you want more details. (I'll be away the next week, so
don't worry if you don't get a fast answer.)

 Best whishes
      Arvid Soderhall

On Tue, 18 Mar 2003, Gemma Kinsella wrote:

> Hi all,
>
> I know that this subject has been on the mailing list before, but I
> couldn't find any response in the archives.
>
> Does anyone have a leap library file or top/crd combination for DMPC or
> other lipids? Either as the single lipid or as a bilayer. Also is there anyone
> out there working on parameterization of these lipids with the Amber force
> field?
>
> Many thanks for all your help,
>
> Gemma Kinsella
>