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

Justin Lemkul jalemkul at vt.edu
Thu Apr 4 14:54:21 CEST 2013

On 4/4/13 5:50 AM, rama david wrote:
> 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.

The command issued depends on what you're doing.  If you want help in that 
respect, post the command that you're using and seek specific assistance.  There 
are too many permutations of possibly "correct" ways of doing something for me 
to offer you a guess.

The input file is simple.  It can be one of two forms:

time  x  y

or simply:

x  y

In the latter case, use the -notime option of g_sham.

Choose your favorite parsing language to extract values from the output of 
g_energy, g_rms, etc to create the combined file.



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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