Hi,
First, I made a small mistake earlier: the potential boost is applied
when your energy is *below* the threshold energy of course. In your
case where you are using potential + dihedral boost (iamd=3), the
potential boost is only applied if the total PE plus the dihedral
boost energy is below the PE threshold. Since your dihedral boost
energies are so large the total is never below your threshold. You may
want to adjust your parameters so that the dihedral boost energies are
smaller.
On Tue, Nov 18, 2014 at 9:49 AM, Aldo Segura <asegurac666.yahoo.com.mx> wrote:
> Sorry for the messed up message. In your experience, is it possible to add
> multiples of alphaP to EthreshP to get higher potential boost? Thank you so
> much for your hep.
Remember, the form of the boost used in Amber is:
(Ethresh - V)^2 / (alpha + (Ethresh - V)
So increasing alpha gets you closer to the original potential surface
(less boost). In my experience with aMD I've found it best to run
several short simulations (something that can finish in less than an
hour), adjusting the alpha and threshold parameters until I've got
boost energies that appear reasonable to me. It also may be helpful
for you to start with just potential (iamd=1) or dihedral (iamd=2)
boosts by themselves before trying the combined boost.
Hope this helps,
-Dan
>
> Best,
>
> Aldo
>
> =======================================
> Aldo Segura-Cabrera
> Postdoctoral Fellow
> Division of Experimental Hematology and Cancer Biology
> Cancer and Blood Diseases Institute
> Cincinnati Children's Hospital Medical Center
> 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
> =========================================
>
> ________________________________
> De: Daniel Roe <daniel.r.roe.gmail.com>
> Para: Aldo Segura <asegurac666.yahoo.com.mx>; AMBER Mailing List
> <amber.ambermd.org>
> Enviado: Martes, 18 de noviembre, 2014 10:01:20
> Asunto: Re: [AMBER] aMD on Amber 12
>
> 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:
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>> mso-header-margin:36.0pt; mso-footer-margin:36.0pt;
>> mso-paper-source:0;}div.WordSection1 {page:WordSection1;}-->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)
>
--
-------------------------
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 - 10:00:06 PST
