- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Vaibhav Dixit <vaibhavadixit.gmail.com>

Date: Sun, 1 Nov 2020 11:35:54 +0530

Dear All,

I'm now able to estimate E differences between the two-states which are

very much in the expected range of 0.7 eV.

I will try the pmemd.MPI option for SP Es, but this choice raises another

query for which I can't quickly find the most updated answer.

There were some very old discussions for differences in sander and pmemd

based E-estimates (here <http://ambermd.org/Questions/mail/308.html>).

Can someone please update me what is expected with Amber18 and newer

versions?

Are the sander and pmemd Es expected to be highly similar and thus one can

ignore whether these E are derived from sander, pmemd (serial, MPI) or even

cpptraj as Adrian suggested to try out?

Or one should use a consistent/identical protocol for estimating Es

especially when one wants to extract/compare differences between two

trajectories or states (and when the expect avg, variance, std are not

known)?

Looking forward to receiving valuable suggestions and guidance from the

list.

Thank you all (and Adrian for valuable suggestions earlier).

Best regards

On Sat, Oct 31, 2020 at 9:58 PM Adrian Roitberg <roitberg.ufl.edu> wrote:

*> Hi
*

*>
*

*> There is a chance that the pmemd.MPI code also does imin=5. If if it
*

*> does, it should accelerate things a lot. The code GPU for sure does not
*

*> do it.
*

*>
*

*> I am not sure how it works, but I believe you could also do it with
*

*> cpptraj itself.
*

*>
*

*> Adrian
*

*>
*

*>
*

*> On 10/30/20 4:56 PM, Vaibhav Dixit wrote:
*

*> > [External Email]
*

*> >
*

*> > Another quick question, is it true that only sander can run single point
*

*> > energy calculations and thus one can only use the CPUs via sander.MPI
*

*> > Is it possible to use the GPU codes to accelerate the calculations?
*

*> > For this system 40 na MD simulation took 2.5 hours, but the imin=5 jobs
*

*> are
*

*> > taking longer.
*

*> > Suggestions on how to speed up the single point energy calculations are
*

*> > highly appreciated.
*

*> > Thanks a lot again.
*

*> > Best regards.
*

*> >
*

*> > On Sat, Oct 31, 2020, 01:50 Vaibhav Dixit <vaibhavadixit.gmail.com>
*

*> wrote:
*

*> >
*

*> >> 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=
*

*> >>>
*

*> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_vaibhav-2Ddixit-2Db1a07a39_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=7elssQ4F84WBiNsfljTDy8jm5OeNxg2-ddO_0zZxSRc&s=_40FGFkj-y7ySGgq344nNaqRYk461VSgWnJZ4jmEmFM&e=
*

*> >>>> ORCID ID:
*

*> >>>
*

*> https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0003-2D4015-2D2941&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=7elssQ4F84WBiNsfljTDy8jm5OeNxg2-ddO_0zZxSRc&s=fOajwbmoQhlzgKNElTGF6jevwgdnSyVn7e1oJrzHf9g&e=
*

*> >>>>
*

*> >>>
*

*> https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.co.in_citations-3Fuser-3DX876BKcAAAAJ-26hl-3Den-26oi-3Dsra&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=7elssQ4F84WBiNsfljTDy8jm5OeNxg2-ddO_0zZxSRc&s=UwwtRBxXH24F_LytzaBDgEQ3qZsGsKfOyMFt3lSLd-I&e=
*

*> >>>> P Please consider the environment before printing this e-mail
*

*> >>>> _______________________________________________
*

*> >>>> AMBER mailing list
*

*> >>>> AMBER.ambermd.org
*

*> >>>>
*

*> >>>
*

*> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=7elssQ4F84WBiNsfljTDy8jm5OeNxg2-ddO_0zZxSRc&s=xNMhALyt9Lo9pqYlEufGhiCypLbo_EE3pL4zkqWmrCc&e=
*

*> >>>
*

*> >>> --
*

*> >>> Dr. Adrian E. Roitberg
*

*> >>> V.T. and Louise Jackson Professor in Chemistry
*

*> >>> Department of Chemistry
*

*> >>> University of Florida
*

*> >>> roitberg.ufl.edu
*

*> >>> 352-392-6972
*

*> >>>
*

*> >>>
*

*> >>> _______________________________________________
*

*> >>> AMBER mailing list
*

*> >>> AMBER.ambermd.org
*

*> >>>
*

*> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=0c-xBcFKyghYKD61RKV_FkPlbFV8wF07crWAhM67oMo&s=-WzwZTVMujjB-8HOUBUkRXQSNpCxo2NcLbix2kFSPsI&e=
*

*> >>>
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> >
*

*> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=0c-xBcFKyghYKD61RKV_FkPlbFV8wF07crWAhM67oMo&s=-WzwZTVMujjB-8HOUBUkRXQSNpCxo2NcLbix2kFSPsI&e=
*

*>
*

*> --
*

*> Dr. Adrian E. Roitberg
*

*> V.T. and Louise Jackson Professor in Chemistry
*

*> Department of Chemistry
*

*> University of Florida
*

*> roitberg.ufl.edu
*

*> 352-392-6972
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Sun, 1 Nov 2020 11:35:54 +0530

Dear All,

I'm now able to estimate E differences between the two-states which are

very much in the expected range of 0.7 eV.

I will try the pmemd.MPI option for SP Es, but this choice raises another

query for which I can't quickly find the most updated answer.

There were some very old discussions for differences in sander and pmemd

based E-estimates (here <http://ambermd.org/Questions/mail/308.html>).

Can someone please update me what is expected with Amber18 and newer

versions?

Are the sander and pmemd Es expected to be highly similar and thus one can

ignore whether these E are derived from sander, pmemd (serial, MPI) or even

cpptraj as Adrian suggested to try out?

Or one should use a consistent/identical protocol for estimating Es

especially when one wants to extract/compare differences between two

trajectories or states (and when the expect avg, variance, std are not

known)?

Looking forward to receiving valuable suggestions and guidance from the

list.

Thank you all (and Adrian for valuable suggestions earlier).

Best regards

On Sat, Oct 31, 2020 at 9:58 PM Adrian Roitberg <roitberg.ufl.edu> wrote:

-- 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Oct 31 2020 - 23:30:02 PDT

Custom Search