Fwd: [gmx-users] Monitoring the water movement during simulation

[bharat gupta]

---------- Forwarded message ----------
From: bharat gupta <bharat.85.monu at gmail.com>
Date: Sun, Jan 30, 2011 at 9:30 PM
Subject: Re: [gmx-users] Monitoring the water movement during simulation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


I tracked the movement of water molecules around residues 65 to 67 of my
protein (GFP crystal structure) .. According to the literature water should
not enter the protein (reason being the cage like structure of GFP) .. but
in VMD, 2 water molecules have been tracked to interact with chromophore ...
So , I am a bit confused as it should not have happened ?? ... For my
analysis  I need to check whether the water is entering the protein or not
.. Since I have simulated some variant structures (long loops) of GFP and I
need to check how this structure would or would not lead to the entrance of
water ??

On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> 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
>
>
>
> 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, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
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-- 
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, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com




-- 
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, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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