Nmodes

&nmode namelist variables¶

Basic input options¶

nmstartframe

Frame number to begin performing nmode calculations on

Note

This variable will choose a subset of the frames chosen from the variables in the &general namelist. Thus, the "trajectory" from which snapshots will be chosen for nmode calculations will be the collection of snapshots upon which the other calculations were performed.

nmendframe (Default = 1000000)

Frame number to stop performing nmode calculations on

Note

This variable will choose a subset of the frames chosen from the variables in the &general namelist. Thus, the "trajectory" from which snapshots will be chosen for nmode calculations will be the collection of snapshots upon which the other calculations were performed.

nminterval (Default = 1)

Offset from which to choose frames to perform nmode calculations on

Note

This variable will choose a subset of the frames chosen from the variables in the &general namelist. Thus, the "trajectory" from which snapshots will be chosen for nmode calculations will be the collection of snapshots upon which the other calculations were performed.

Parameter options¶

nmode_igb (Default = 1)

Value for Generalized Born model to be used in calculations. Options are:

• 0: Vacuum
• 1: HCT GB model

nmode_istrng (Default = 0.0)

Ionic strength to use in nmode calculations. Units are Molarity (M). Non-zero values are ignored if nmode_igb is 0 above.

dielc (Default = 1.0)

Distance-dependent dielectric constant

drms (Default = 0.001)

Convergence criteria for minimized energy gradient.

maxcyc (Default = 10000)

Maximum number of minimization cycles to use per snapshot in sander.