I request TI experts on the list to please comment and give me some
valuable suggestions on the following.
thank you and best regards.
On Thu, Oct 22, 2020 at 2:57 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> 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
>
> P Please consider the environment before printing this e-mail
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
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
P Please consider the environment before printing this e-mail
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Received on Mon Oct 26 2020 - 04:00:02 PDT
