[gmx-users] About Free energy surface .....g_sas

[rama david]

Thank you justin,

I read the  articles, archive and also g_sham -h,

As I mentioned in previous mail, I simulated four random coil peptide ,
they started to form
Beta sheet structure after 20 ns ..( simulation time 100ns )

My interest is how to draw the Free energy diagram for Potential energy and
Structures...(eg.  RMSD, Gyrate, different cluster ,
with different structure at particular time ) .


Would you please tell me how to do it in gromacs with command line and
needed input.

I tried it a lot but not able to find the way  ..


I will be a very grateful to you for ur help ..


With best Regards
Rama david.







On Thu, Apr 4, 2013 at 1:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/4/13 2:14 AM, rama david wrote:
>
>> Dear Friends,
>>    I simulated the 4 peptide in water box .
>> As they come close to each other they start to from anti-parallel
>> beta sheet structure.
>>
>>
>>
>> Now I want to draw the Free energy surface for the
>> same ..How is  there pot energy ???
>>
>> Would you please tell me how to do it ..
>>
>> ( I read about g_sham -h, I tried it, but not understand properly)
>>
>> I will be very grateful for your suggestion and help..
>>
>>
> The logic behind g_sham was just posted to this list no more than a few
> days ago.
>
> http://lists.gromacs.org/**pipermail/gmx-users/2013-**March/079810.html<http://lists.gromacs.org/pipermail/gmx-users/2013-March/079810.html>
>
> It calculates a free energy surface as a function of two variables of your
> choosing.  As David noted (http://lists.gromacs.org/**
> pipermail/gmx-users/2013-**March/079813.html<http://lists.gromacs.org/pipermail/gmx-users/2013-March/079813.html>),
> the result may not correspond to a true quantitative representation of free
> energy differences, though.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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