# FEP with slow-growth method

**URL:** <https://gromacs.bioexcel.eu/t/fep-with-slow-growth-method/1536>\
**Category:** User discussions\
**Created:** [February 3, 2021, 3:33pm UTC](https://gromacs.bioexcel.eu/t/fep-with-slow-growth-method/1536 "2021-02-03T15:33:53Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![mehr](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mehr/32/547_2.png) [@mehr](https://gromacs.bioexcel.eu/u/mehr)\
**Post date:** [February 3, 2021, 3:33pm UTC](https://gromacs.bioexcel.eu/t/fep-with-slow-growth-method/1536/1 "2021-02-03T15:33:53Z")

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GROMACS version: 2020.3

Dear all,

I am calculating free energy perturbation (FEP) for converting state A to state B and vice versa using the following for the free energy variables in the mdp file:

free-energy = yes  
init-lambda = 0 (and 1 for B state)  
delta-lambda = 1e-5 (and -1e-5 for B state)  
sc-alpha = 0.3  
sc-sigma = 0.25  
sc-power = 1  
couple-lambda0 = vdw-q  
couple-lambda1 = none  
couple-intramol = yes  
nstcalcenergy = 1  
nstdhdl = 1

It seems that the equilibration and transition runs go well, but I have problems with analyzing the results.  
My question is if it’s possible to use “gmx bar” to analyze such a system? And if not, what are the alternatives?

Thanks,  
Mehrnoosh

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [February 4, 2021, 3:34pm UTC](https://gromacs.bioexcel.eu/t/fep-with-slow-growth-method/1536/2 "2021-02-04T15:34:24Z")

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Hi,

> My question is if it’s possible to use “gmx bar” to analyze such a system?

No

> And if not, what are the alternatives?

You can use gmx energy -odh to extract dh/dl

Best regards  
Alessandra

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**Author:** ![mehr](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mehr/32/547_2.png) [@mehr](https://gromacs.bioexcel.eu/u/mehr)\
**Post date:** [February 5, 2021, 10:36am UTC](https://gromacs.bioexcel.eu/t/fep-with-slow-growth-method/1536/3 "2021-02-05T10:36:10Z")

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Dear Alessandra,

Thank you so much for your reply.

Can you explain a bit more how I can use gmx energy? Now I have several xvg files as my output for different frames that I got from gmx mdrun -dhdl frame{i}.xvg; and there is no dH data in my edr files. Are my mdrun calculations wrong?

Thank you for your time.

Best regards,  
Mehrnoosh