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