Hi Trevor,
I request to elaborate it a little bit more. It is ok for persons having
great hand with amber but for for beginners, it may be not so clear that how
to use these three lines.. what will be the input and what will be the
output. Please suggest the tutorial if you can.
Thanks,
Hirdesh
On Wed, Sep 22, 2010 at 10:52 AM, Trevor Gokey <tgokey.mail.sfsu.edu> wrote:
> Hello,
>
> Someone else asked a very similar question recently....
>
> try this:
>
> center origin .CA
> image origin center familiar
> rms first .CA
>
> The rms command will make it easy to see water near a point on your
> protein.
>
> -Trevor
> ________________________________________
> From: Ye MEI [ymei.itcs.ecnu.edu.cn]
> Sent: Sunday, September 19, 2010 8:02 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] molecular dynamics simulation-water-box-diffution
> problem
>
> keep in mind that each water molecule stands for itself and its images in
> all the periodic cell units.
>
>
> 2010-09-20
>
>
>
> Ye MEI
>
>
>
> From: Rilei Yu
> Date: 2010-09-20 10:53:47
> To: amber
> CC:
> Subject: [AMBER] molecular dynamics simulation-water-box-diffution problem
>
> Dear amber users,
> After simulation on my protein for 10ns, I found water molecules diffuse
> considerably. When I tried to analysis it in the VMD, keeping water with 5
> angstrom distance from the protein, I could only find several water
> molecules. To solve this problem, I have checked the mail-list, and found
> some people suggest use iwrap=1.
> But here I still have some questions:
> 1 Although, the water molecules diffused considerably, the dynamics
> property of my protein was normal.
> 2 In fact I adopted the md simulation parameters from the tutorial:
> http://ambermd.org/tutorials/basic/tutorial1/section6.htm. I found in the
> tutorial the water molecules also diffuse to some degree in the 120 ps MD.
> So any one can give some criteria on my problem? Can I ignore it?
> Very appreciated for your help!
> Rilei Yu
>
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Received on Tue Sep 21 2010 - 23:00:03 PDT
