Re: Peptide in Membrane Environment: loosing water from one leaflet

From: bo liu (
Date: Mon Apr 20 2009 - 08:35:33 CDT

Hi Praveen,

Your system seems to suffer from center of mass drifting (in z direction),
you may want to use zeroMomentum on in the configuration file.


2009/4/20 Praveen Agrawal <>

> Hi,
> I am simulating small protein helix (42 amino acids) in membrane
> environment. Till now it has completed some 50ns of simulation. It
> seems that one of the leaflet is loosing water to the other leaflet
> resulting in thickening of leaflet and thinning of the other. Is it
> normal? (It seems so if I reason that because of periodic box
> condition the two leaflets are anyway joined). I am new to membrane
> simulation and any guidance would be really helpful.
> Best Regards,
> Praveen

-Bo Liu
Graduate Student
Theoretical and Computational Biophysics
GUCAS, CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety
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