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

[bharat gupta]

I followed the lysozyme tutorial step by step and everything seems to be
fine and the literature cannot be wrong as it has been proved ..
I have repeated this simulation second time... I want to ask one thing that
during solvation step and equilibration step water is mixed with the protein
so it means that the structure should not have water inside it during
equilibration step itself or not ?

On Sun, Jan 30, 2011 at 10:50 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> I followed the lysozyme tutorial step by step and everything seems to be
> fine and the literature cannot be wrong as it has been proved ..
> I have repeated this simulation second time... I want to ask one thing that
> during solvation step and equilibration step water is mixed with the protein
> so it means that the structure should not have water inside it during
> equilibration step itself or not ?
>
>
> On Sun, Jan 30, 2011 at 10:34 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
>
>>
>>
>> On 01/31/11, *bharat gupta * <bharat.85.monu at gmail.com> wrote:
>>
>>
>>
>> ---------- 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 ??
>>
>>
>> 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:
>>
>>>
>>>
>>>
>>> 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
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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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