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
Received on Sat Oct 31 2020 - 09:30:02 PDT
