Re: [AMBER] aMD on Amber 12 from Daniel Roe on 2014-11-18 (Amber Archive Nov 2014)

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 18 Nov 2014 08:01:20 -0700

Hi,

Your email came in very garbled (missing newlines etc) which made it
difficult to parse. If possible try to send things to the list in
plain text format in the future.

That said, you certainly have differences in your dihedral energies:

> DIHED = 15848.4365 # Non-aMD
> DIHED = 47360.5197 # aMD

and if you check your aMD log you'll see that you are indeed getting a
big dihedral boost (last number):

> 5000 785000 -480647.202895273920 47120.363307878375 1.000000000000 0.000172857168 0.000000000000 129716.426811902173

You're not getting any potential boost (second to last number) because
the PE hasn't risen above your specified threshold (-477022).

-Dan

On Mon, Nov 17, 2014 at 10:53 PM, Aldo Segura <asegurac666.yahoo.com.mx> wrote:
> Hello everyone, I am trying to do sometests with aMD on amber 12. I already did 200 ns simulation on this protein-ligand systemusing pmemd.cuda. So, I tried to follow the manual instructions to perform aMDon it, but it seems is not working because I did not notice any differencerespect to the simulation using pmemd.cuda alone. As the manual suggested, I addedto Eb(dih) multiples of alpha (2X, 4X, 6X, 10X…) for higher acceleration andthere is no difference in the results. Here is the information of my system and the inpunt for pmemd.cuda:
> no. of atoms: 168207
>
> no. of residues (ligand included): 1491
>
> ave_epot: -510662.9304
>
> ave_dihe: 15864.5125
>
>
> 3.5 * 1491= 5218.5
>
> alphaD = (1/5) * 5218.5 = 1043.7
>
> EthreshD = 5218 + 15864 = 21082
>
> alphaP = 168207 * (1/5) = 33641.4
> EthreshP = -510662.9304 + 33641 = -477021.9304
>
>
>
> ig=-1,
> imin=0,irest=1,ntx=5,
> nstlim=125000000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=1.0, ioutfm=1, iwrap=1,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> iamd=3,
> ethreshd=21082, alphad=1044,
> ethreshp=-477022, alphap=33641,
> /
>
> Here is a fragment ofthe output using pmemd.cuda alone: NSTEP = 815000 TIME(PS) = 2230.000 TEMP(K) = 300.42 PRESS = -126.8 Etot = -406789.1395 EKtot = 103958.8672 EPtot = -510748.0067 BOND = 4728.6164 ANGLE = 12275.8411 DIHED = 15848.4365 1-4 NB = 5330.5300 1-4 EEL = 51522.3414 VDWAALS = 58875.0408 EELEC = -659328.8129 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 43215.3845 VIRIAL = 47899.2587 VOLUME = 1711491.0577 Density = 1.0067 ------------------------------------------------------------------------------ NSTEP = 820000 TIME(PS) = 2240.000 TEMP(K) = 299.74 PRESS = 90.3 Etot = -407887.6661 EKtot = 103723.1797 EPtot = -511610.8458 BOND = 4629.2373 ANGLE = 12106.4622 DIHED = 15802.9587 1-4 NB = 5406.0596 1-4 EEL = 51590.1358 VDWAALS = 60204.5597 EELEC = -661350.2590 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 43260.6577 VIRIAL = 39921.4369 VOLUME = 1712767.3543 Density = 1.0059 ------------------------------------------------------------------------------ Here is a fragment ofthe output using pmemd.cuda with aMD: NSTEP = 815000 TIME(PS) = 2230.000 TEMP(K) = 301.06 PRESS = -29.9 Etot = -376495.0744 EKtot = 104180.2891 EPtot = -480675.3635 BOND = 4565.2249 ANGLE = 13367.1498 DIHED = 47360.5197 1-4 NB = 5208.1735 1-4 EEL = 50696.1713 VDWAALS = 59502.2362 EELEC = -661374.8389 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 43190.7528 VIRIAL = 44297.6105 VOLUME = 1712793.4145 Density = 1.0059 ------------------------------------------------------------------------------ NSTEP = 820000 TIME(PS) = 2240.000 TEMP(K) = 300.10 PRESS = 9.4 Etot = -377241.0533 EKtot = 103849.7734 EPtot = -481090.8268 BOND = 4705.3342 ANGLE = 13608.3724 DIHED = 47322.2061 1-4 NB = 5160.5467 1-4 EEL = 50426.2493 VDWAALS = 59466.8915 EELEC = -661780.4270 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 43372.3488 VIRIAL = 43023.7008 VOLUME = 1710416.9243 Density = 1.0073 ------------------------------------------------------------------------------ This is a lastfragment of the amd.log file: bash-4.1$ tail amd.log 5000 785000 -480647.202895273920 47120.363307878375 1.000000000000 0.000172857168 0.000000000000 129716.426811902173 5000 790000 -481134.391026637983 47257.762343714014 1.000000000000 0.000173456921 0.000000000000 129485.995137548394 5000 795000 -480395.602210825775 47564.722687611356 1.000000000000 0.000174808146 0.000000000000 128971.193002039130 5000 800000 -480571.340056136716 47377.097419776954 1.000000000000 0.000173980361 0.000000000000 129285.858609870047 5000 805000 -480442.272442598362 47055.138141021132 1.000000000000 0.000172573546 0.000000000000 129825.815869500351 5000 810000 -479886.118565759622 48143.936395731755 1.000000000000 0.000177401190 0.000000000000 127999.797599786805 5000 815000 -480675.363465000410 47360.519683936611 1.000000000000 0.000173907505 0.000000000000 129313.661078757083 5000 820000 -481090.826785803307 47322.206079091877 1.000000000000 0.000173739297 0.000000000000 129377.916713270373 5000 825000 -480271.830837909132 47518.834657253698 1.000000000000 0.000174605148 0.000000000000 129048.151615417257 5000 830000 -480790.213786629494 47371.100524365902 1.000000000000 0.000173954000 0.000000000000 129295.915984160965 I would appreciate anyhelp with this issue. Best, Aldo =======================================
> Aldo Segura-Cabrera
> Postdoctoral Fellow
> Division of Experimental Hematology and Cancer BiologyCancer and Blood Diseases Institute
> Cincinnati Children's Hospital Medical Center
> 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
> =========================================
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Nov 18 2014 - 07:30:03 PST