Re: [gmx-users] questions in Running MDS over docked poses

[Justin A. Lemkul]

vivek sharma wrote:

hi Justin,
Thanks for your reply...
I am interested in looking for the stability of the docked pose, by 
applying some temperature variation in the molecule.
If I am applying temperature variation then should I use pressure 
coupling simultaneously.


Well that's going to depend on how much you're varying the temperature.  I have 
a colleague who has done some thermal stability simulations upwards of 600K and 
the NPT algorithm breaks down (using AMBER).  I don't know if that's true of the 
Gromacs code as well.



Can you suggest some tutorial for such attempts.



Well, I don't know about tutorials, but (again depending on how much you're 
varying the temperature) some of the literature regarding thermal stability of 
proteins over wide temperature ranges might be of interest.


-Justin


With Thanks,
Vivek

2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED] >



vivek sharma wrote:

Hi There,
I am running MDS over the docked poses to check the stability of
the docked poses using gromacs.
I have few doubts about selecting parameters for the same, If
anybody have tried such thing earlier, please suggest me for the
same.

Should I keep pressure coupling over the simulation ?


Sure; life exists at NPT, so it is commonly used in routine protein
simulations.


For how long should I run the simulation for such purpose ?


That's up to you :)  You should run the simulations as long as you
feel necessary to achieve stability.  I know that's vague, but there
really is no single correct answer to this question in the MD field.
 If there is, I'd love for someone to tell me, too...;)

-Justin

Waiting for suggestions.

With Thanks,
Vivek




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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] questions in Running MDS over docked poses

[vivek sharma]

hi Justin,
Thanks for your reply...
I am interested in looking for the stability of the docked pose, by applying
some temperature variation in the molecule.
If I am applying temperature variation then should I use pressure coupling
simultaneously.
Can you suggest some tutorial for such attempts.

With Thanks,
Vivek

2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]>

>
>
> vivek sharma wrote:
>
>> Hi There,
>> I am running MDS over the docked poses to check the stability of the
>> docked poses using gromacs.
>> I have few doubts about selecting parameters for the same, If anybody have
>> tried such thing earlier, please suggest me for the same.
>>
>> Should I keep pressure coupling over the simulation ?
>>
>
> Sure; life exists at NPT, so it is commonly used in routine protein
> simulations.
>
>  For how long should I run the simulation for such purpose ?
>>
>>
> That's up to you :)  You should run the simulations as long as you feel
> necessary to achieve stability.  I know that's vague, but there really is no
> single correct answer to this question in the MD field.  If there is, I'd
> love for someone to tell me, too...;)
>
> -Justin
>
>  Waiting for suggestions.
>>
>> With Thanks,
>> Vivek
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> interface or send it to [EMAIL PROTECTED]
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] questions in Running MDS over docked poses

[Justin A. Lemkul]

vivek sharma wrote:

Hi There,
I am running MDS over the docked poses to check the stability of the 
docked poses using gromacs.
I have few doubts about selecting parameters for the same, If anybody 
have tried such thing earlier, please suggest me for the same.


Should I keep pressure coupling over the simulation ?


Sure; life exists at NPT, so it is commonly used in routine protein simulations.


For how long should I run the simulation for such purpose ?



That's up to you :)  You should run the simulations as long as you feel 
necessary to achieve stability.  I know that's vague, but there really is no 
single correct answer to this question in the MD field.  If there is, I'd love 
for someone to tell me, too...;)


-Justin


Waiting for suggestions.

With Thanks,
Vivek




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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] questions in Running MDS over docked poses

[vivek sharma]

Hi There,
I am running MDS over the docked poses to check the stability of the docked
poses using gromacs.
I have few doubts about selecting parameters for the same, If anybody have
tried such thing earlier, please suggest me for the same.

Should I keep pressure coupling over the simulation ?
For how long should I run the simulation for such purpose ?

Waiting for suggestions.

With Thanks,
Vivek
___
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