[gmx-users] Regarding 1-d free energy profile from g_sham

bipin singh bipinelmat at gmail.com
Sat Apr 5 06:39:08 CEST 2014


Hi Richa,

I was not able to get exactly what I wanted. As you know the g_sham output
does not give you the energy Vs PC information, rather it gives energy Vs
bin index information. So, the problem is how to transform bin index
information into PC values.

As I was not much interested in exact PC values, so I have tried to find
out the PC values where the system spends most of the time (from the PC Vs
time plot), once we find those PC values, then one can approximately map
minimas in 1-d FEL to the corresponding approximate range of PC values.
Again I will say this not the most accurate way of getting PC Vs energy
information. For getting exact information there is no way to get it
directly from g_sham without post processing its output as suggested by Dr.
Justin.


On Fri, Apr 4, 2014 at 5:43 PM, richa <richa.s.rathorerr at gmail.com> wrote:

> Hi Bipin,
>
> Just went through your post. I also have the similar issue of making 1 D
> free energy plots. I tried it with g_sham and got a file which contains the
> bin index and 3 more columns. But I want the energies as a function of the
> principal component I'm using.
>
> Could you please help me if you were able to plot the 1 D free energy
> surfaces?
>
> thanks and regards
> Richa
>
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-- 



*--------------------Thanks and Regards, Bipin Singh*


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