CST:Utilities

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CST Utilities

• accu-info
• accu-combine
• accu-trajectory
• pmf-integrate
• pmf-energy
• aus-integrate

The CST data can be processed be the following utilities.

• CST accumulator processing (only if freadranges is on).
  • accu-info
  • accu-combine
  • accu-trajectory
• The free energy, internal energy, entropic contribution and other data:
  • pmf-integrate
  • pmf-energy
  • aus-integrate

pmf-integrate

pmf-integrate supports the following integration realms. The updated list can be shown by the --listrealms option.

# Realm              Method Description                                           
# ------------------ ------ ------------------------------------------------------
mTdS/dx              CST    -TdS(x)=|Cov(lam,H) dx]/RT + TdS{CST}corr (TDS subsystem)
-TdS/dx              CST    -TdS(x)=|Cov(lam,H) dx|/RT + TdS{CST}corr (TDS subsystem)
-TdS/dx(VF)          CST    -TdS(x)=|[<ICFK>_FW + cov(ICF,Eint)_FW/(k_B*T)]dx| (VF subsystem)
mTdS/dx(VF)          CST    -TdS(x)=|[<ICFK>_FW + cov(ICF,Eint)_FW/(k_B*T)]dx| (VF subsystem)
dA/dx(VF)            CST    dA(x)=|<ICFFW> dx| (VF subsystem)
dA/dx                CST    dA(x)=|<lam> dx| + dA{CST}corr (MD subsystem)
dA/dx(TDS)           CST    dA(x)=|<lam> dx| + dA{CST}corr (TDS subsystem)
dU/dx                CST    dU=|[<ICFP>_FW - cov(ICF,Eint)_FW/(k_B*T)] dx| (VF subsystem)
dU/dx(VF)            CST    dU=|[<ICFP>_FW - cov(ICF,Eint)_FW/(k_B*T)] dx| (VF subsystem)
dMICF/dx             CST    |<ICF> dx| (VF subsystem)
dMICFFW/dx           CST    |<ICF>_FW dx| (VF subsystem)
dMICFKFW/dx          CST    |<ICFK>_FW dx| (VF subsystem)
dMICFPFW/dx          CST    |<ICFP>_FW dx| (VF subsystem)
dLAMBDA/dx(MD)       CST    |<lambda> dx| (MD subsystem)
dLAMBDA/dx(TDS)      CST    |<lambda> dx| (TDS subsystem)
C11II                CST    |cov(ICF,Eint)/(k_B*T) dx| (VF subsystem)
C11IIFW              CST    |cov(ICF,Eint)_FW/(k_B*T) dx| (VF subsystem)
C11KIFW              CST    |cov(ICFK,Eint)_FW/(k_B*T) dx| (VF subsystem)
C11PIFW              CST    |cov(ICFP,Eint)_FW/(k_B*T) dx| (VF subsystem)
C11LI                CST    |cov(lambda,Eint)/(k_B*T) dx| (TDS subsystem)
C11LK                CST    |cov(lambda,Ekin)/(k_B*T) dx| (TDS subsystem)
C11LP                CST    |cov(lambda,Epot)/(k_B*T) dx| (TDS subsystem)
C11LR                CST    |cov(lambda,Erst)/(k_B*T) dx| (TDS subsystem)
C11LT                CST    |cov(lambda,Etot)/(k_B*T) dx| (TDS subsystem)
C11LTFW              CST    |cov(lambda,Etot)_FW/(k_B*T) dx| (TDS subsystem)

pmf-energy

pmf-energy supports the following energy realms. The updated list can be shown by the --listrealms option.

# Realm              Method Description                                           
# ------------------ ------ ------------------------------------------------------
-TdS_corr            CST    -TdS{CST}corr
mTdS_corr            CST    -TdS{CST}corr
<Eint>               CST    <Eint>
<Eint>FW             CST    <Eint>_FW
<Ekin>               CST    <Ekin>
<Ekin>FW             CST    <Ekin>_FW
<Epot>               CST    <Epot>
<Epot>FW             CST    <Epot>_FW
<Erst>               CST    <Erst>
<Erst>FW             CST    <Erst>_FW
<Etot>               CST    <Etot>
<Etot>FW             CST    <Etot>_FW
dA_corr              CST    dA{CST}corr
dA_corr(TdS)         CST    dA{CST}corr (TDS subsystem)
dU                   CST    dU=<Etot>_FW