From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Nov 29 2016 - 11:09:40 CST
Another point in addition to those mentioned ....
What water model are you using ? Models such as TIP3P and SPC are rigid,
so unless you are using a fully flexible water model, I'd argue that you
should constrain hydrogen atoms to correctly represent the water model ....
On 11/29/2016 05:16 PM, Axel Kohlmeyer wrote:
> On Tue, Nov 29, 2016 at 5:54 AM, Harish Srinivasan
> <harishlglk1992_at_gmail.com> wrote:
>> I am trying simulate micellar systems like SDS, SDBS micelle in water. I
>> equilibrated the system for 20 ns using NPT Langevin piston.
>> Even after 20 ns run, the average temperature remained at 295 K for the
>> system (I am still pondering why this happened), so I used rescale velocity
>> (with rescalefreq 2 timesteps) for 500 ps.
>> After this I ran a NVE simulation (meaning, i switched off all the
>> thermostats and barostats) for about another 20 ns, the total energy of the
>> system seemed to change about 20000 units in the span of 20 ns.
>> I am using 1 fs timestep, with 2fs for non-bonded forces and 4fs for full
>> electrostatics. No rigidity imposed.
> 1 fs is far too large a time step for unconstained hydrogen atoms. try
> something in the range 0.25 - 0.5fs
>> Thank you,
-- Dr. Vlad Cojocaru Computational Structural Biology Laboratory Department of Cell and Developmental Biology Max Planck Institute for Molecular Biomedicine Röntgenstrasse 20, 48149 Münster, Germany Tel: +49-251-70365-324; Fax: +49-251-70365-399 Email: vlad.cojocaru[at]mpi-muenster.mpg.de http://www.mpi-muenster.mpg.de/43241/cojocaru
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