> yes, that's probably right. I use 60 for POPE, and it turns out to be
> single layer...... so it is different from GAFF.
Yes, the lipid 11 force field is based on GAFF parameters but it is NOT
GAFF. My apologies on the paper not being out yet. We are trying very hard
to get it published but running into much resistance.
> Moreover, the surface tension values probably should also have
> something
> to do with the cutoff we use..... I don't know whether Ross have any
> comments on this aspects.
No it should NOT depend on the cutoff. Why would you think it should depend
on the cutoff?
If it does then your cutoff is TOO SMALL, period!
I suggest you check things carefully. Ultimately if you want to publish the
work you will need to defend the surface tension you used so you might as
well run a few hundred nanoseconds for the system you want to run with a
range of surface tension values and then you'll be able to provide a
justification of the value you used if a reviewer asks.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 15 2012 - 03:30:04 PDT
