Friendly bump ... ;-)
On 3/6/19 10:18 AM, David Bickel wrote:
> Dear Amber-team,
>
> I encountered a problem running simulations of a membrane system with
> distance restraints on GPUs. My system consists of a natural product
> molecule (750 Da) in the center of a membrane. The goal is to perform a
> steered MD, pulling the ligand from the membrane into the solvent.
>
> The system was set up using packmol-memgen from AmberTools.
>
> For equilibration, I first performed a minimization, a short NVT MD for
> heating, and a NPT MD for the density equilibration on CPUs using pmemd.MPI.
> For the MD steps, I used distance restraints (fxyz=0,0,1) between the
> COM of the molecule (:1) and the phosphor atoms of the lipids (@P31), in
> order to keep the molecule in the center of the membrane.
>
> Now I wanted to switch to pmemd.cuda to equilibrate the system for
> further 50 ns under NTP conditions, using the same distance restraints
> as above. However, when running the system on GPUs the RESTRAINT energy
> immediately overflows (within 1 step), while the corresponding
> DUMPAVE-file still shows reasonable z-values. Eventually such a system
> would blow up and cancel.
>
> Starting the same calculation with pmemd.MPI works fine and returns
> output as expected.
>
> I tried equilibrating the system for further 10 ns on CPUs, before
> switching to GPUs, but the issue remains the same.
> I tried using different parameters for the constant pressure-condition
> as well as disabling iwrap. No success either.
> I also tried running the simulation on different clusters with different
> Amber-builds (Amber18 & 17) under different UNIX-evironments. In any
> case the result was the same, pmemd.cuda does not work while pmemd.MPI does.
> Assuming, that the error is in my restraint definition, I also tried
> defining the distance restraint towards the phosphor atoms of one
> leaflet only. Still no, success.
> By chance, I realized, that modifying the ligand atom selection in my
> restraint file to the first 8 atoms (IGR1(1-8)) gets the system running
> on GPUs. The initial reaction coordinate is ~4 A then and thus, the
> restraint energy starts at ~80 kcal/mol. However, the system is running
> just fine and the ligand gradually reorients to better fulfill the
> restraints.
>
> Does anyone have an idea, where the issue might be located? I would be
> very grateful for any suggestions.
>
> Below, I'll append all input/output files mentioned above.
>
> Best regards,
> David Bickel
>
> #
> # -- MD INPUT FILE
> #
> > NPT MD for 9,000 ps for equilibration
> > &cntrl
> > ntx = 5,
> > irest = 1, iwrap = 0,
> >
> > ntpr = 1,
> > ntwx = 5,
> >
> > nstlim = 4500000,
> > t = 1000.0,
> > dt = 0.002,
> >
> > ntt = 3,
> > gamma_ln = 2.0,
> > temp0 = 300.0, tempi = 300.0,
> >
> > ntb = 2,
> > barostat = 1, pres0 = 1.0, comp = 44.6, taup = 1.0,
> > ntp = 3, csurften = 3, gamma_ten = 0.0, ninterface = 2,
> >
> > ntc = 2, ntf = 2,
> > tol = 0.000001,
> >
> > nmropt = 1,
> > /
> > &wt type='DUMPFREQ',
> > istep1=1,
> > /
> > &wt type='END',
> > /
> > DISANG=pxa_00_5kcal.rst
> > DUMPAVE=06_ntp_equi.rstout
> > LISTIN=POUT
> > LISTOUT=POUT
>
>
> #
> # --- RESTRAINT FILE "pxa_00_5kcal.rst"
> #
> > &rst iat=-1,-1,0
> > r1=-50.000000, r2=0.000000, r3=0.000000, r4=50.000000,
> rk2=5.000000, rk3=5.000000,
> > iresid=0,
> > fxyz=0,0,1,
> > outxyz=1,
> >
> IGR1(1)=1,IGR1(2)=2,IGR1(3)=3,IGR1(4)=4,IGR1(5)=5,IGR1(6)=6,IGR1(7)=7,IGR1(8)=8,IGR1(9)=9,IGR1(10)=10,IGR1(11)=11,IGR1(12)=12,IGR1(13)=13,IGR1(14)=14,IGR1(15)=15,IGR1(16)=16,IGR1(17)=17,IGR1(18)=18,IGR1(19)=19,IGR1(20)=20,IGR1(21)=21,IGR1(22)=22,IGR1(23)=23,IGR1(24)=24,IGR1(25)=25,IGR1(26)=26,IGR1(27)=27,IGR1(28)=28,IGR1(29)=29,IGR1(30)=30,IGR1(31)=31,IGR1(32)=32,IGR1(33)=33,IGR1(34)=34,IGR1(35)=35,IGR1(36)=36,IGR1(37)=37,IGR1(38)=38,IGR1(39)=39,IGR1(40)=40,IGR1(41)=41,IGR1(42)=42,IGR1(43)=43,IGR1(44)=44,IGR1(45)=45,IGR1(46)=46,IGR1(47)=47,IGR1(48)=48,IGR1(49)=49,IGR1(50)=50,IGR1(51)=51,IGR1(52)=52,IGR1(53)=53,IGR1(54)=54,IGR1(55)=55,IGR1(56)=56,IGR1(57)=57,IGR1(58)=58,IGR1(59)=59,IGR1(60)=60,IGR1(61)=61,IGR1(62)=62,IGR1(63)=63,IGR1(64)=64,IGR1(65)=65,IGR1(66)=66,IGR1(67)=67,IGR1(68)=68,IGR1(69)=69,IGR1(70)=70,IGR1(71)=71,IGR1(72)=72,IGR1(73)=73,IGR1(74)=74,IGR1(75)=75,IGR1(76)=76,IGR1(77)=77,IGR1(78)=78,IGR1(79)=79,IGR1(80)=80,IGR1(81)=81,IGR1(82)=82,IGR1(83)=83,IGR1(84)=84,IGR1(85)=85,IGR1(86)=86,IGR1(87)=87,IGR1(88)=88,IGR1(89)=89,IGR1(90)=90,IGR1(91)=91,IGR1(92)=92,
> >
> IGR2(1)=151,IGR2(2)=285,IGR2(3)=419,IGR2(4)=553,IGR2(5)=687,IGR2(6)=821,IGR2(7)=955,IGR2(8)=1089,IGR2(9)=1223,IGR2(10)=1357,IGR2(11)=1491,IGR2(12)=1625,IGR2(13)=1759,IGR2(14)=1893,IGR2(15)=2027,IGR2(16)=2161,IGR2(17)=2295,IGR2(18)=2429,IGR2(19)=2563,IGR2(20)=2697,IGR2(21)=2831,IGR2(22)=2965,IGR2(23)=3099,IGR2(24)=3233,IGR2(25)=3367,IGR2(26)=3501,IGR2(27)=3635,IGR2(28)=3769,IGR2(29)=3903,IGR2(30)=4037,IGR2(31)=4171,IGR2(32)=4305,IGR2(33)=4439,IGR2(34)=4573,IGR2(35)=4707,IGR2(36)=4841,IGR2(37)=4975,IGR2(38)=5109,IGR2(39)=5243,IGR2(40)=5377,IGR2(41)=5807,IGR2(42)=5932,IGR2(43)=6057,IGR2(44)=6182,IGR2(45)=6307,IGR2(46)=6432,IGR2(47)=6557,IGR2(48)=6682,IGR2(49)=6807,IGR2(50)=6932,IGR2(51)=7057,IGR2(52)=7182,IGR2(53)=7307,IGR2(54)=7432,IGR2(55)=7557,IGR2(56)=7682,IGR2(57)=7807,IGR2(58)=7932,IGR2(59)=8057,IGR2(60)=8182,IGR2(61)=8307,IGR2(62)=8441,IGR2(63)=8575,IGR2(64)=8709,IGR2(65)=8843,IGR2(66)=8977,IGR2(67)=9111,IGR2(68)=9245,IGR2(69)=9379,IGR2(70)=9513,IGR2(71)=9647,IGR2(72)=9781,IGR2(73)=9915,IGR2(74)=10049,IGR2(75)=10183,IGR2(76)=10317,IGR2(77)=10451,IGR2(78)=10585,IGR2(79)=10719,IGR2(80)=10853,IGR2(81)=10987,IGR2(82)=11121,IGR2(83)=11255,IGR2(84)=11389,IGR2(85)=11523,IGR2(86)=11657,IGR2(87)=11791,IGR2(88)=11925,IGR2(89)=12059,IGR2(90)=12193,IGR2(91)=12327,IGR2(92)=12461,IGR2(93)=12595,IGR2(94)=12729,IGR2(95)=12863,IGR2(96)=12997,IGR2(97)=13131,IGR2(98)=13265,IGR2(99)=13399,IGR2(100)=13533,IGR2(101)=13963,IGR2(102)=14088,IGR2(103)=14213,IGR2(104)=14338,IGR2(105)=14463,IGR2(106)=14588,IGR2(107)=14713,IGR2(108)=14838,IGR2(109)=14963,IGR2(110)=15088,IGR2(111)=15213,IGR2(112)=15338,IGR2(113)=15463,IGR2(114)=15588,IGR2(115)=15713,IGR2(116)=15838,IGR2(117)=15963,IGR2(118)=16088,IGR2(119)=16213,IGR2(120)=16338,
> > nstep1=0, nstep2=0,
> > &end
>
>
> #
> # --- STARTING CONDITIONS FROM MDOUT
> #
> > R1 = -99.000 R2 = 0.000 R3 = 0.000 R4 = 99.000 RK2 = 5.000
> RK3 = 5.000
> > Rcurr: 0.037 Rcurr-(R2+R3)/2: 0.037
> MIN(Rcurr-R2,Rcurr-R3): 0.037
>
>
> #
> # --- RESULTS FROM MDOUT
> #
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> --------------------------------------------------------------------------------
> >
> >
> >
> > NSTEP = 1 TIME(PS) = 925.002 TEMP(K) = 298.48 PRESS
> = 24.9
> > Etot = ************** EKtot = 25421.1250 EPtot =
> **************
> > BOND = 2076.2292 ANGLE = 8505.3570 DIHED
> = 5083.6430
> > 1-4 NB = 1858.0038 1-4 EEL = -22464.4248 VDWAALS
> = 4273.3586
> > EELEC = -98833.1557 EHBOND = 0.0000 RESTRAINT =
> **************
> > EAMBER (non-restraint) = -99500.9889
> > EKCMT = 7057.5051 VIRIAL = 6851.8744 VOLUME =
> 382196.4740
> > SURFTEN = 30.6828
> > Density = 1.0174
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.015 Angle = 0.000 Torsion =
> 0.000
> >
> ===============================================================================
> >
> > NSTEP = 2 TIME(PS) = 925.004 TEMP(K) = 297.72 PRESS
> = -4.3
> > Etot = ************** EKtot = 25356.4648 EPtot =
> **************
> > BOND = 2095.6856 ANGLE = 8523.1258 DIHED
> = 5092.7207
> > 1-4 NB = 1861.4326 1-4 EEL = -22455.4085 VDWAALS
> = 4265.0974
> > EELEC = -98822.5718 EHBOND = 0.0000 RESTRAINT =
> **************
> > EAMBER (non-restraint) = -99439.9183
> > EKCMT = 7037.1397 VIRIAL = 7072.4544 VOLUME =
> 382197.2895
> > SURFTEN = -1.2366
> > Density = 1.0174
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 0.016 Angle = 0.000 Torsion =
> 0.000
> >
> ===============================================================================
> >
> [...]
>
>
> #
> # --- DUMPAVE 06_ntp_equi.rstout
> #
> > 0 x: 0.679 y: 0.728 z: 0.056 0.997
> > 1 x: 0.679 y: 0.729 z: 0.056 0.998
> > 2 x: 0.680 y: 0.730 z: 0.056 0.999
> > 3 x: 0.680 y: 0.731 z: 0.057 1.000
> > 4 x: 0.681 y: 0.732 z: 0.057 1.001
> > 5 x: 0.682 y: 0.733 z: 0.058 1.002
> > 6 x: 0.683 y: 0.733 z: 0.059 1.003
> > 7 x: 0.683 y: 0.733 z: 0.060 1.004
> > 8 x: 0.684 y: 0.732 z: 0.062 1.004
> > 9 x: 0.684 y: 0.732 z: 0.063 1.004
> [...]
>
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Received on Fri Mar 08 2019 - 07:30:02 PST
