[AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Wed, 4 Jun 2014 00:30:21 +0300


Is lipid14 fully compatible with AMBER12 for production runs?
In addition are lipid11 and lipid14 compatible with NAMD v2.10? I am doing
a simulation using lipid11 in NAMD but I 've heard from a colleague that
the electrostatic scaling factor (scee) and the van der Waals scaling
factor (scnb) are not computed in the same way as in AMBER. He didn't know
exactly though what happens. Aren't these parameters defined explicitly in
the .prmtop file so that NAMD could know how to compute the vdW and
electrostatics correctly, or does the code override them?

And one final thing, rather irrelevant to the above: are there any
pre-equilibrated lipid14 or lipid11 mebranes with cholesterole?

I would be grateful if someone clarified those things for me.


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Jun 03 2014 - 15:00:02 PDT
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