Hi Mark,
What you are seeing is because Leap is over zealous on avoiding clashes at
the edge of the box. If you only run NVT you will have a density of just
0.78 or so which leads to the formation of vacuum bubbles that you are
seeing. The solution is to run a quick NPT run as soon as you can to
equilibrate the density. Then you can switch back to NVT. I would suggest:
1) Minimize
2) 20ps or so heat to 300K NVT
3) 100ps NPT (or until the density has equilibrated) at 300K
4) NVT, NVE, NPT, your choice.
Note you should also image your trajectory using ptraj before visualizing it
to make sure you are viewing just the central cell.
As for Langevin piston pressure control, this is not supported by sander.
Just use ntb=2,ntp=1 for 100ps or so and you should be good.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Mark M Huntress
> Sent: Saturday, February 27, 2010 1:46 PM
> To: AMBER Mailing List
> Subject: RE: [AMBER] swiss cheese water shell
>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> -------------------------------------------------
> 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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