VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 03 2011 - 05:04:23 CST

On Mon, Jan 3, 2011 at 5:15 AM, Sibel Cakan <sibelc_at_stu.khas.edu.tr> wrote:
>
> Dear all
> I’m trying to run a residue-based CG MD simulation with NAMD for a system
> which includes waters, proteins, and a lipid  bilayer.During the MD
> simulation I had several problems and I had checked this page

please post questions about NAMD to the NAMD mailing list.

> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting and
> the mailing list which reccomends to do heating protocol.So I tried the
> heating protocol and assign the temperature from 30 to 323 K.But in the log
> file the temperature could not reach the 323K(the temperature was ~270-280)
> and the simulation gives error that 'Atoms moving too fast' .

that means, that your system has high potential energy.
this is best removed by minimizing. it may be needed to
minimize multiple times. for a multi-component system,
it is often a good idea to keep components in place and
only gradually release them with position restraints (which
are called constraints in NAMD-speak) whose strength
is gradually removed.

axel.
> Could somebody help me out? Thanks a lot. 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.