Dear Amber developers and experts,
I have done the following for running TI calculations with the model-Heme
system.
1) A single pdb file containing ions was created for both the Heme redox
states and parameters were loaded for both.
2) Then water-box was added and prmtop/inpcrd file was created such that
both states are present in one prmtop file.
3) Now the two following md-input files were used to run pmemd.cuda jobs.
Can you please suggest to me which one is the correct usage and more likely
to give me meaningful free E predictions? I'm guessing that I need to take
the difference of DV/DL values for the two TI-regions.
thank you
First MD input file:
&cntrl
nstlim =3000000, nscm=2000,
ntx=1, irest=0, ntpr=1000,
tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
ntb=1, igb=0, cut=8.0,
dt=0.001, ioutfm=1, iwrap=1,
ntc=2, ntf=1,
ntwr = 10000, ntwx=1000, ntave=1000
icfe = 1, ifsc = 1,
timask1=':1-5', scmask1=':1-3',
timask2=':6-10', scmask2=':6-8',
/
Second MD input file:
&cntrl
nstlim =3000000, nscm=2000,
ntx=1, irest=0, ntpr=1000,
tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
ntb=1, igb=0, cut=8.0,
dt=0.001, ioutfm=1, iwrap=1,
ntc=2, ntf=1,
ntwr = 10000, ntwx=1000, ntave=1000
icfe = 1, ifsc = 1,
timask1=':1-5', scmask1=':1-3',
timask2=':6-10', scmask2=':6-8',
ifmbar = 1,
mbar_states = 15,
mbar_lambda = 0.00, 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, 1.00,
/
--
Regards,
Dr. Vaibhav A. Dixit,
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Thu Oct 22 2020 - 06:30:02 PDT
