Hello again,
so I found that the ir6 restraint is implemented, and it works for me when I use 50 or fewer atoms for the two groups in the pulling simulation. However, when I use more I get the previously mentioned error:
'Error: an illegal memory access was encountered launching kernel kCalculateNMREnergy'
I found the cuda file, where I think the ir6 routine is implemented (/apps/amber/amber20_src/src/pmemd/src/cuda/kCNF.h). From my understanding, there is no limit to the number of interatomic distances set, like in the CPU version.
________________________________
Von: Niklas Halbwedl
Gesendet: Montag, 4. März 2024 09:54:45
An: amber.ambermd.org
Betreff: ir6 restraint with pmemd.cuda problem
Dear all,
I am trying to run a pulling simulation in AMBER20 using the ir6=1 restraint. This works fine on CPU, but does not work using pmemd.cuda. My question is, whether this restraint is even implemented for GPU.
The error I get is: Error: an illegal memory access was encountered launching kernel kCalculateNMREnergy
Thanks for your help,
Niklas Halbwedl
TUM
******My input file:**********
Pre HREUS-Run with COM-Pulling for Adv-FE-Calculation
&cntrl
! GENERAL FLAGS DESCRIBING THE CALCULATION
imin=0,
nmropt=1,
! NATURE AND FORMAT OF THE INPUT
irest=1,
ntx=5,
ntwr=1000, ! Number of timesteps to write out a backup restrt file
ntwx=1000,
! NATURE AND FORMAT OF THE OUTPUT
ntxo=2,
ntpr=1,
iwrap=0,
! FROZEN OR RESTRAINT ATOMS
ntr=1,
restraint_wt=2,
restraintmask=':1-611&!.H=',
! MOLECULAR DYNAMICS
nstlim=5,
dt=0.0001,
! TEMPERATURE REGULATION
ntt=3,
temp0=300.0,
tautp=2.0,
gamma_ln=5
! PRESSURE REGULATION
ntp=0,
! SHAKE BOND LENGTH CONSTRAINTS
ntc=2,
! POTENTIAL FUNCTION PARAMETERS
ntf=2,
ntb=1,
dielc=1.0,
cut=9.0,
/
&wt type = 'REST', istep1 = 0, istep2 = 1, value1 = 1.0, value2 = 1.0,/
&wt type='DUMPFREQ', istep1=1,/
&wt type = 'END',/
DUMPAVE=com_pull.txt
DISANG=test2.rof
***Restraint file***
&rst
iat=-1,-1, nstep1=1, nstep2=100000, ifvari=1, ninc=100,ir6=1, ! COM-Restr. /w 1000incrmts evry 100stps
r1=0.00, r2=12.725, r3=12.725, r4=99.00, rk2=0.00000, rk3=0.00000, ! nstep1 Anchor Pos+Strngth for harm. pot.
r1a=0.0, r2a=2.00000, r3a=2.00000, r4a=99.0, rk2a=2.00, rk3a=2.00, ! nstep2 Anchor Pos+Strngth for harm. pot.
! Atom IDs for calculation of COM Positions of the pocket
igr1=2118,2124,2125,2126,2127,2133,2163,2164,2166,2167,2168,2169,2170,2171,2172,2173,2174,2175,2176,2180,2183,2226,2227,2228,2230,2231,2232,2233,2234,2235,2236,2237,2238,2239,2240,2241,2242,2809,2810,2811,2813,2814,2815,2816,2817,2818,2820,2821,2823,2825,2826,2827,2846,2857,2858,2860,2861,2862,2863,2864,2865,2866,2867,2869,2910,2916,2921,2933,2934,2935,3597,6209,6210,6211,6213,6214,6215,6217,6218,6220,6221,6257,6258,6259,6260,6262,6263,6264,6268,6269,6270,6271,6272,6273,6274,6275,6277,6279,6280,6281,6282,6283,6322,6323,6324,6325,6326,6327,6328,6329,6330,6331,6332,6333,6343,6344,0,
! Atom IDs for calculation of COM Positions of the peptide
igr2=9952,9953,9954,9955,9956,9957,9958,9959,9960,9961,9962,9963,9964,9965,9966,9967,9968,9969,9970,9971,9972,9973,9974,9975,9976,9977,9978,9979,9980,9981,9982,9983,9984,9985,9986,0,
/
&rst
iat=-1,-1, nstep1=100001, nstep2=250000,ir6=1, ! const. COM-Restr. from step 100001
r1=0.0, r2=2.00000, r3=2.00000, r4=99.0, rk2=2.00, rk3=2.00, ! Anchor Pos+Strngth for harm. pot.
! Atom IDs for calculation of COM Positions of the pocket
igr1=2118,2124,2125,2126,2127,2133,2163,2164,2166,2167,2168,2169,2170,2171,2172,2173,2174,2175,2176,2180,2183,2226,2227,2228,2230,2231,2232,2233,2234,2235,2236,2237,2238,2239,2240,2241,2242,2809,2810,2811,2813,2814,2815,2816,2817,2818,2820,2821,2823,2825,2826,2827,2846,2857,2858,2860,2861,2862,2863,2864,2865,2866,2867,2869,2910,2916,2921,2933,2934,2935,3597,6209,6210,6211,6213,6214,6215,6217,6218,6220,6221,6257,6258,6259,6260,6262,6263,6264,6268,6269,6270,6271,6272,6273,6274,6275,6277,6279,6280,6281,6282,6283,6322,6323,6324,6325,6326,6327,6328,6329,6330,6331,6332,6333,6343,6344,0,
! Atom IDs for calculation of COM Positions of the peptide
igr2=9952,9953,9954,9955,9956,9957,9958,9959,9960,9961,9962,9963,9964,9965,9966,9967,9968,9969,9970,9971,9972,9973,9974,9975,9976,9977,9978,9979,9980,9981,9982,9983,9984,9985,9986,0,
****End of Output file****
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 730.010 TEMP(K) = 302.37 PRESS = 0.0
Etot = -315557.1070 EKtot = 73627.8516 EPtot = -389184.9586
BOND = 1883.9725 ANGLE = 5101.2498 DIHED = 7934.7348
1-4 NB = 2347.0697 1-4 EEL = 28228.3618 VDWAALS = 47800.0436
EELEC = -482480.3908 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
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Received on Fri Mar 08 2024 - 04:00:02 PST
