[gmx-users] re: genbox -shell

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 16 09:09:36 CET 2005

Dongsheng Zhang wrote:
> 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.)

I'm sorry but you'll have to check the source code then.

> 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!
Not convenient. We usually apply high pressure after solvating in a 
shell which will make the box collapse in a few 100 ps.

>>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.
>>>gmx-users mailing list
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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