Dear Adrian
Sorry for the confusion, I wanted to say that the two prmtop files are
identical with respect to topology but different with respect to cofactor
charges.
Yes I understand that it might make sense to run imin=5 jobs for both
trajectories using both prmtop, especially if I want the output inside the
two mdout files to be comparable snapshot by snapshot.
Thanks a lot for explaining me about this.
I try these options asap and get back to the list in case of further
queries.
Thanks a lot again.
Best regards
On Fri, Oct 30, 2020, 22:41 Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi
>
> A couple of things.
>
> First, I presume this is wrong.
>
> "For this, I have ensured that prmtop files for both states are identical."
>
> If they are identical, then you will get the EXACT same answer for the
> same geometry for both states, which is not what you want, agree ?
>
>
> Second: imin=5 does not give you EKtot, etc because there is NO velocity
> information in your dynamics file, just coordinates, so the only thing
> you can compute is the potential energy.
>
> Third, I would do imin=5 with your two prmtops.
>
> There is a chance that your mdout and mdcrd files are offset, maybe by
> just one frame, so you could get in trouble.
>
> Just run MD with prmtop_1, save mdcrd, and do TWO imin=5 runs, one with
> prmtop_1 and one with prmtop_2
>
> Makes sense ?
>
> Adrian
>
>
> On 10/30/20 1:05 PM, Vaibhav Dixit wrote:
> > [External Email]
> >
> > Dear Amber experts,
> > I'm trying to estimate the vertical energy gap as defined in Figure 4 of
> this
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pubs.acs.org_doi_10.1021_acs.chemrev.5b00298-23-5Fi25&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=7elssQ4F84WBiNsfljTDy8jm5OeNxg2-ddO_0zZxSRc&s=EQNT92U8KcAapBIsufQtRliHoFCdD0ZtVfR_8EX3xC0&e=
> >paper.
> > For this, I have ensured that prmtop files for both states are identical.
> > Then, I've used imin=5 prmtop of 1st state to re-calculate Amber energies
> > at the coordinate of the 2nd state.
> > I'm getting the following energies for the two states.
> > The mdin file is also shown below. Can you please suggest to me if these
> > results seem meaningful? I can't see the Etot, EKtot and EPtot values in
> > the mdout file while using imin=5. Did I miss/missunderstand the usage of
> > some keywords/options in mdin file while using imin=5?
> > Input file for 1st state normal md is given at the bottom of the message.
> >
> > Looking forward to receiving valuable suggestions from the list.
> >
> > *mdin file*
> > single point energy calculations of 1st state coordinates using
> parameters
> > of the 2nd state
> > &cntrl
> > ntx=1, ntpr=1, ntwx=1,
> > imin=5, maxcyc=1, !Single-point energy calculation on each frame
> > ntb=0, !Non-periodic
> > cut=9999., !Calculate all solute-solute interactions
> > /
> >
> > *Energies for 1st state while using normal MD:*
> > NSTEP = 10000 TIME(PS) = 1050.000 TEMP(K) = 299.32 PRESS =
> > 0.0
> > Etot = -49685.1834 EKtot = 12894.9072 EPtot =
> > -62580.0906
> > BOND = 404.7503 ANGLE = 1270.4594 DIHED =
> > 1749.3757
> > 1-4 NB = 514.7171 1-4 EEL = 7140.6069 VDWAALS =
> > 7564.3402
> > EELEC = -81224.3402 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> >
> ------------------------------------------------------------------------------
> >
> > *Energies of 1st state while using 2nd state prmtop and imin=5*
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 1 -5.6620E+04 1.3817E+01 1.2211E+02 CG 286
> >
> > BOND = 401.5878 ANGLE = 1266.0832 DIHED =
> > 1754.2166
> > VDWAALS = 7317.4110 EEL = -75019.9377 HBOND =
> > 0.0000
> > 1-4 VDW = 516.7397 1-4 EEL = 7144.3101 RESTRAINT =
> > 0.0000
> > minimization completed, ENE= -.56619589E+05 RMS= 0.138167E+02
> > minimizing coord set # 2
> >
> >
> > Maximum number of minimization cycles reached.
> >
> > Normal MD input file for 1st state:
> > Production Stage in Explicit Solvent
> > &cntrl
> > ntt=3, ! Temperature scaling (=3, Langevin dynamics)
> > gamma_ln=2.0, ! Collision frequency of the Langevin dynamics in
> ps-1
> > ntc=2, ! SHAKE constraints (=2, hydrogen bond lengths
> > constrained)
> > ntf=2, ! Force evaluation (=2, hydrogen bond interactions
> > omitted)
> > ntb=1, ! Boundaries (=1, constant volume)
> > cut=10.0, ! Cutoff
> > dt=0.002, ! The time step in picoseconds
> > nstlim=20000000, ! Number of MD steps to be performed
> > ig=-1, ! Random seed (=-1, get a number from current date
> and
> > time)
> > ntwr=10000, ! Restart file written every ntwr steps
> > ntwx=10000, ! Trajectory file written every ntwx steps
> > ntpr=10000, ! The mdout and mdinfo files written every ntpr steps
> > ioutfm=1, ! Trajectory file format (=1, Binary NetCDF)
> > iwrap=1, ! Translate water molecules into the original
> simulation
> > box
> > igb=0, ! GB model (=0, explicit solvent)
> > irest=1, ! Flag to restart the simulation
> > ntx=5, ! Initial condition (=5, coord. and veloc. read from
> the
> > inpcrd file)
> > /
> > Thank you and best regards.
> >
> > --
> >
> > 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
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bits-2Dpilani.ac.in_pilani_vaibhavdixit_profile&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=7elssQ4F84WBiNsfljTDy8jm5OeNxg2-ddO_0zZxSRc&s=-pG_lhiTbOUelpfEFTLNbg6OH5CFKEWt1sk9eMYQKgM&e=
> >
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>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Fri Oct 30 2020 - 13:30:02 PDT
