[gmx-users] re: genbox -shell

Dongsheng Zhang dong at pampas.chem.purdue.edu
Fri Dec 16 05:04:14 CET 2005

Dear David,

my question is why a few water molecules are out of the shell if I use
gnebox -shell command. To my understanding, all water molecules should
be inside the shell. If the shell is full of water, then no more water
can be added to the box, is it right? (I keep asking this question
because I want to know how genbox works. In fact I have trouble to use
this method to solvate my system.)

The following is my second question. I'd like to ask you for your
suggestion. If I solvate the peptoid molecule in a shell of water,only
part of peptoid will be hydrated after I run NVT MD for a short time
because the dynamic of water is much faster than the peptoid. If I run
the simulation with pressure coupling, the length of peptoid will be
greater than the length of box. I am thinking to solvate the peptoid
molecule by adding water full of box (about 20000 water molecules), then
I will manually remove some water (e.g. 1000 at each step) step by step
with a short NPT MD simulation (10 ps) to relax the system. This method
is not so convenient.Do you have any suggestion? thanks!

> --
> Message: 5
> Date: Thu, 15 Dec 2005 22:09:46 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re. genbox -shell
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43A1DB9A.5090100 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> Mark Abraham wrote:
> > Dongsheng Zhang wrote:
> > 
> >> Dear David,
> >>
> >> I am confused by your reply. In your tutorial, you use
> >> editconf .. -c -d 0.5
> >>
> >> Now I am using -d 1.0, and 1.0 nm = 10 A, I don't understand why you
> >> think the box is too small.
> > 
> > 
> > A pertinent question is whether your shell is large enough to model 
> > long-range electrostatics reasonably. I suspect you'd have a heavy 
> > majority of people in this decade thinking that 1.0nm is not enough.
> > 
> but this was an extended peptide, and it will collapse. Good way to make 
> a starting structure for folding simulations.
> > Mark
> > _______________________________________________
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Dongsheng Zhang <dong at pampas.chem.purdue.edu>

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