I am curious do you refer TI specifically?
Is FEP implemented in Amber? I also want to run FEP with Amber, would love
to hear your thoughts.
On Tue, Aug 8, 2023 at 5:42 PM 东庚 via AMBER <amber.ambermd.org> wrote:
> Dear Amber community,
> I'm trying to run the SQM/MM FEP calculations. The version I am using is
> Amber22. The simulation process is calculated using Sander.MPI.
>
> When I generated an input file using the new version of the mbar method in
> the Amber22 manual, an error was reported('error in reading namelist
> cntrl').
> Here is the input file:
> ##########################################
> NPT simulation
> &cntrl
> irest=0,ntx=1,
> nstlim=50000,dt=0.002,
> temp0=300.0,ntt=3,gamma_ln=2.0,
> ntc=2,ntf=1,
> cut=8.0,
> ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
> icfe=1,clambda = 0.5,
> ifmbar=1,
> mbar_states = 15,
> mbar_lambda = 0.01, 0.05, 0.10, 0.15, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70,
> 0.80, 0.85, 0.90, 0.95, 0.99,
> ifsc=1,scmask=":PHN.O1,H6",
> ifqnt = 1,
> /
> &qmmm
> qmmask=':PHN.1-13',
> qmcharge=0,
> qm_theory='DFTB3’,
> /
> ##########################################
> And my terminal's command is
> ' mpirun -np 2 sander.MPI -ng 2 -groupfile group_prod_l ‘ .
>
> When I generate an input file using the old version of Amber formate, it
> can be run. The input file is as follows:
> ##########################################
> NPT simulation
> &cntrl
> irest=0,ntx=1,
> nstlim=500000,dt=0.001,
> temp0=300.0,ntt=3,gamma_ln=2.0,
> ntc=2,ntf=1,
> cut=8.0,
> ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
> icfe=1,clambda = 0.5,
> ifmbar=1,
> bar_intervall=1000,bar_l_min=0.005,bar_l_max=0.995,bar_l_incr=0.1,
> ifsc=1,scmask=":BNZ.H6",
> ifqnt = 1,
> /
> &qmmm
> qmmask=':BNZ.1-12',
> qmcharge=0,
> qm_theory='DFTB3',
> /
> ##########################################
>
> I confused than I can only use the old formate of lambda setting with
> sander.MPI.
>
> Best Regards,
> Geng
>
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Received on Wed Aug 16 2023 - 08:00:02 PDT
