Dear All,
I have been experiencing the same thing (zeros everywhere and no free
energy is collected) when trying to perform TI using sander. I perform
minimization and equilibration (as I would do for a simulation) before
the TI step.
Could someone help and perhaps post an input for sander TI (and perhaps
also the min and equil input before that) applicable to a protein?
Regards,
Annette
Xiao He wrote:
>Dear Amber users,
> I want to use thermodynamic free energy calculations,
>
>I read the manual and try a system like this
>
> nstlim=1000,ntpr=100
> icfe=1,
> clambda=0.5,
> klambda=4,
> ntb=0,
> temp0 = 300.0, tautp = 1.0,
> ntf = 2, ntc = 2,
> dt = 0.002,
> ntave = 25,
>
>But it seems it does not calculate the free energy.
>
> DV/DL, AVERAGES OVER 25 STEPS
>
>
> NSTEP = 25 TIME(PS) = 0.050 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
>
>Would anyone like to tell me how to do it properly?
>Thanks for your reply.
>
>Best wishes,
> Xiao He
> hx.itcc.nju.edu.cn
> 2004-11-02
>
>
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Received on Tue Nov 02 2004 - 11:53:00 PST
