[gmx-users] free energy perturbation

Yuhua Song yhsong at ccb.wustl.edu
Mon Oct 27 16:49:01 CET 2003

Hi, Anton:

Thanks for the kind reply.

>  > I am doing some FEP work with Gromacs. According to one reply in the
> [...]
>  > Could you please to take a look to see what is wrong about the
>  > that I had done?
> First off, you can check your .tpr files with 'gmxcheck -s 1.tpr -s2
> (check the exact options) and see if the differences between them are what
> they should be.

I had checked the way that you mention, it did have the difference between
them as they should be.

When I use "g_energy -f 1.edr -f2 2.edr -fee -s 1.tpr" to get the
runavgdf.xvg about the free energy information. The first coloumn shows the
time, the second coloumn shows the the potential energy difference between
two states: E1-E2, the third couloum shows the free energy differnce, my
understanding is right?

Also, when use the "mdrun -rerun ..." way, it is very quickly for me to get
the free energy perturbation if my understanding as described above is
right, and the method that I used that is described in the previous e-mail
is right.

My question is: then what will be the difference for geting the free energy
perturbation with the thermodynamics integration way? because thermodynamics
Integration way will involve at least another 2ns calculation. If there is
no advantage for thermodynamics integration way, then why bother to use TI
way to get free energy perturbation other than the way using the
mdrun -rerun way?

Also, when I use: "g_rms -f 1.trr -f2 2.trr -s 1.tpr" to compare the
comformation change, it always reach more than 3A, it seems too big, when I
use:" g_confrms -f1 1.gro -f2 2.gro" to compare them, I also get the similar
value, When I check the energy etc. values, no abrupt change. I am not quite
sure, what is wrong here, when I read the mailing list, it seems that there
are different way to calculate the conformation change, it will get
different results. There are other ways that I can do to get the reasonable
conformational change?

Thank you very much,


> -- 
> Groetjes,
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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