ah yes. I should do that, thank you. Could I also use Langevin piston for pressure control, after the system is heated? Is there an essential difference between using langevin piston or using NTP=1? I mean, some disadvantage to using langevin?
Thank you
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of Barbault Florent [florent.barbault.univ-paris-diderot.fr]
Sent: Saturday, February 27, 2010 6:48 AM
To: AMBER Mailing List
Subject: Re: [AMBER] swiss cheese water shell
Hello,
This looks like a NVT simulation, isn't it? In this case switch on NTP
in order to get better density around your protein. I hope this will
help you.
Regards
Florent Barbault
On Sat, 27 Feb 2010 00:40:25 -0500
Mark M Huntress <markmh.bgsu.edu> wrote:
> Hi, I have a 10Å TIP3P water solvent shell around a protein, and I
>did MD on just the waters, freezing the protein, with periodic
>boundary conditions, with slow heat, so I turned off Langevin. After
>500 ps the edges of the solvent cube have developed a couple big
>empty spaces, and the cube looks like a block of swiss cheese.
>Offhand, does anyone have a good idea of what I might have messed up?
> Thanks
> Mark
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-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr
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Received on Sat Feb 27 2010 - 14:00:05 PST
