From: bo liu (liubo.njuer_at_gmail.com)
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.
Best.
Bo
2009/4/20 Praveen Agrawal <praveen.agrawal_at_gmail.com>
> 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 19A Yuquan Road, Beijing 100049, P.R. China Web: http://nanosafety.ihep.ac.cn/ Office: (86)-010-xxxxxxxx Home: (86)-010-88259765 Cell: +86-13426057875
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