I am doing umbrella sampling simulation using CHARMM to obtain PMF between two structures.
rxncor: umbrella kumb 10.0 form 1 del0 5
rxncor: statistics lowdelta 4.0 hidelta 6.0 deldel 0.1
While the simulation set up is fine, I face the following issues.
1. When the del value is 5, as per the definition of UMBR sampling, the distance should be restrained at 5 (between two structures) with fluctuation of +/- deldel values as given in lowdel and highdel values. But a del value of 5 (k_umb=10) samples region in 4 while del value of 6 samples at 5 even with low kumb=2. Does solvent entropy bring in this shift? Is this correct behavior?
2. Though the structures are constrained harmonically with force constant of 100 kcal/mol using CONS HARM command, slight deviation from the reference is observed.. Is it possible to fix the structures but allowing the translation along x direction (rxn coordinate for sampling is distance between two structures along x direction).
Last edited by vidhya; 08/16/20 10:59 AM.