[gmx-users] About Free energy surface .....g_sas
ramadavidgroup at gmail.com
Thu Apr 4 11:50:13 CEST 2013
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
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
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.
> It calculates a free energy surface as a function of two variables of your
> choosing. As David noted (http://lists.gromacs.org/**
> the result may not correspond to a true quantitative representation of free
> energy differences, though.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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