[gmx-users] Monitoring the water movement during simulation

[Mark Abraham]

On 01/31/11, bharat gupta  <bharat.85.monu at gmail.com> wrote:
> Hi,
> 
> I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ??
> 
> 

Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD.

Mark

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> Pls help
> 
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> 
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
> 
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> 
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