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

rama david ramadavidgroup at gmail.com
Thu Apr 4 15:37:55 CEST 2013

Thank you a lot justin for offering me help.

I am interested to use g_sham ..( And if the other command give me my
output, I am also interested to know the other  way )

I was confuse with the input that I have to give with g_sham.

I proceed the following command

g_energy is used to get potential ( pot.xvg )
g_rmsdist is used to get rmsdist.xvg
What sis next ????????

My confusion start with the input to give the g_sas ...

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

time  x  y

or simply:

x  y

But what is flag for  command  input and out put.

I also read g_sham -h  and  manual.
Please accept my apology.

I will be grateful to you for help ...

With best regards,
Rama david.

On Thu, Apr 4, 2013 at 6:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==============================**==========
> 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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