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starwingc / peptoid_24summer

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Problem when preparing the FEP file #15

Closed starwingc closed 3 months ago

starwingc commented 3 months ago

Hi @vvoelz ,

When I try to generate the tpr file for FEP, the fatal error go out like:

ERROR 1 [file prod_fep.mdp]:
  initial thermodynamic state 5 does not exist, only goes to 0

please check the peptoid/19AE1-4-A/GAFF/protonated/HREX, and follow the runme.sh and running the ./prepare_tpr.sh

starwingc commented 3 months ago

the fep-lamdas should always keep fix like below:

Contents of prod_fep.mdp in state_5:
free_energy              = yes
calc-lambda-neighbors    = -1
init-lambda-state        = 5

nstdhdl                  = 5000
separate-dhdl-file       = yes
dhdl-print-energy        = total

; lambda-states          = 0     1     2     3     4     5    
fep-lambdas              = 0.00  0.20  0.40  0.60  0.80  1.0