Dear AMBER
In the past few days, I used Amber18's thermodynamic integration method to calculate the free energy change from benzene to phenol using pmemd program in the tutorial. Encountered two problems as follows:
1. The process from benzene to phenol in the tutorial is divided into three steps: decharge, vdw_bonded, and recharge. Can it be achieved in one step? How should the input file parameters be modified?
2. When I tried to compare the results of TI with FEP and BAR using the ifbar parameter, I found that the MBAR energy output by pmemd.mpi of Amber18 is very different from the energy output by pmemd.cuda. Take a system of methane molecules in water box as an example. When lamda=1.0, the energy of pmemd.MPI output file is like this:
MBAR Energy analysis:
Energy at 0.0000 = -48412.8976
Energy at 0.5000 = -48412.4985
Energy at 1.0000 = -48412.0994
The output file of pmemd.cuda is as follows:
MBAR Energy analysis:
Energy at 0.0000 = -45396.9413
Energy at 0.5000 = -48321.2714
Energy at 1.0000 = -48330.8687
Through the calculation of BAR and FEP, I found that the output energy of pmemd.cuda can correctly calculate the solvation free energy of methane molecule (2.00 kcal/mol).
The input file for MD simulation is provided as follows:
fabregas to win
&cntrl
imin=0,irest=1,ntx=5,
ntb=2,cut=11.0,
ntp=1,pres0=1.0,taup=2.0,
ntf=1,ntc=2,
ntt=3,gamma_ln=5,
temp0=300.0,
nstlim=10000000,dt=0.001,
ntpr=1000,ntwr=1000,ntwx=1000,
ifsc=1,icfe=1,clambda=1.0,
timask1=':1',timask2='',
scmask1=':1',scmask2='',
ifmbar=1,mbar_states=3,mbar_lambda=0.0,0.5,1.0,
/
I do not know what's the problem, could any body tell me why?
Thanks in advance
Sincerely;
Wang Bo
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ecnu_wangbo
|
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ecnu_wangbo.126.com
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Received on Tue Sep 01 2020 - 23:00:02 PDT
