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

[Mark Abraham]

On 01/31/11, bharat gupta  <bharat.85.monu at gmail.com> wrote:
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> 
> ---------- 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 ??
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> 

We can't tell. We don't know if your simulation model is flawed, the literature is wrong, your modified GFP do let water in, or your observations of "interacting with the chromophore" aren't right.


>  ... 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 ??
> 
> 

To observe a transit, look for snapshots where they were in one place, and snapshots where they were in another.

Mark


> 
> On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
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> > On 01/31/11, bharat gupta  <bharat.85.monu at gmail.com> wrote:
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> > > 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 ??
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> > Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD.
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> > 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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> 
> -- 
> 
> 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, +82-51-583-8343Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
> 
> 
> 
> 
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