Dear Amber community,
May be somebody knows about the following issue:
pmemd.cuda -O -i prod.in -o prod.out -p bcyd_lig.prmtop -c bcyd_lig_den.rst
-r bcyd_lig_prod1.rst -x prod.nc
+++ Loading the PLUMED kernel runtime +++
+++
PLUMED_KERNEL="/home/dkarlov/soft/plumed-2.6.0/src/lib/libplumedKernel.so"
+++
PLUMED: PLUMED is starting
PLUMED: Version: 2.6.0 (git: Unknown) compiled on Mar 19 2020 at 13:57:52
PLUMED: Please cite these papers when using PLUMED [1][2]
PLUMED: For further information see the PLUMED web page at
http://www.plumed.org
PLUMED: Root: /home/dkarlov/soft/plumed-2.6.0/
PLUMED: For installed feature, see
/home/dkarlov/soft/plumed-2.6.0//src/config/config.txt
PLUMED: Molecular dynamics engine: amber
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 10428
PLUMED: File suffix:
PLUMED: FILE: plumed.dat
PLUMED: Action CENTER
PLUMED: with label cc
PLUMED: serial associated to this virtual atom is 10429
PLUMED: of atoms:
PLUMED: 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
68 69 70
PLUMED: 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
93 94 95
PLUMED: 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112
113 114 115 116 117 118 119 120
PLUMED: 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136
137 138 139 140 141 142 143 144 145
PLUMED: 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161
162 163 164 165 166 167 168 169 170
PLUMED: 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186
187 188 189 190 191 192
PLUMED: using the geometric center
PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
order
PLUMED: Action CENTER
PLUMED: with label cl
PLUMED: serial associated to this virtual atom is 10430
PLUMED: of atoms:
PLUMED: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
PLUMED: 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
PLUMED: using the geometric center
PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
order
PLUMED: Action DISTANCE
PLUMED: with label d
PLUMED: between atoms 10429 10430
PLUMED: using periodic boundary conditions
PLUMED: Action CENTER
PLUMED: with label o5m
PLUMED: serial associated to this virtual atom is 10431
PLUMED: of atoms:
PLUMED: 61 82 103 124 145 166 187
PLUMED: using the geometric center
PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
order
PLUMED: Action CENTER
PLUMED: with label c3m
PLUMED: serial associated to this virtual atom is 10432
PLUMED: of atoms:
PLUMED: 53 74 95 116 137 158 179
PLUMED: using the geometric center
PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
order
PLUMED: Action TORSION
PLUMED: with label a1
PLUMED: between atoms 10431 10432 10 7
PLUMED: using periodic boundary conditions
PLUMED: Action ANGLE
PLUMED: with label a2
PLUMED: between atoms 10431 10432 10430
PLUMED: using periodic boundary conditions
PLUMED: Action METAD
PLUMED: with label metadP
PLUMED: with arguments d a1 a2
PLUMED: added component to this action: metadP.bias
PLUMED: Binsize not specified, 1/5 of sigma will be be used
PLUMED: Gaussian width 0.050000 0.050000 0.025000 Gaussian height
0.300000
PLUMED: Gaussian deposition pace 500
PLUMED: Gaussian file HILLS
PLUMED: Well-Tempered Bias Factor 15.000000
PLUMED: Hills relaxation time (tau) 116.402469
PLUMED: KbT 2.494339
PLUMED: Grid min 0 -pi 0
PLUMED: Grid max 6 pi pi
PLUMED: Grid bin 600 629 629
PLUMED: Grid uses spline interpolation
PLUMED: added component to this action: metadP.work
PLUMED: Bibliography [3][4]
PLUMED: Action PRINT
PLUMED: with label .8
PLUMED: with stride 500
PLUMED: with arguments d a1 a2
PLUMED: on file COLVAR
PLUMED: with format %f
PLUMED: END FILE: plumed.dat
PLUMED: Timestep: 0.002000
PLUMED: KbT: 2.494323
PLUMED: Relevant bibliography:
PLUMED: [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
PLUMED: [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput.
Phys. Commun. 185, 604 (2014)
PLUMED: [3] Laio and Parrinello, PNAS 99, 12562 (2002)
PLUMED: [4] Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603
(2008)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
pmemd.cuda: Plumed.h:2605: plumed_gcreate: Assertion `plumed_gmain.p==NULL'
failed.
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7feb29abb2ed in ???
#1 0x7feb29aba503 in ???
#2 0x7feb28baafcf in ???
#3 0x7feb28baaf47 in ???
#4 0x7feb28bac8b0 in ???
#5 0x7feb28b9c429 in ???
#6 0x7feb28b9c4a1 in ???
#7 0x55acc2998427 in ???
#8 0x55acc299932b in ???
#9 0x55acc29992ef in ???
#10 0x55acc2726e89 in ???
#11 0x55acc275fc52 in ???
#12 0x55acc26ac37e in ???
#13 0x7feb28b8db96 in ???
#14 0x55acc26c29b9 in ???
#15 0xffffffffffffffff in ???
Aborted
I should note that this error does not occur when I use sander instead of
pmemd.cuda
prod.in file contains following information:
cyd metad
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=25000, ntwx=25000,
ntt=3, gamma_ln=2.0,
temp0=300.0, ig=-1,
plumed = 1, plumedfile = 'plumed.dat',
/
--
DK
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 26 2020 - 12:30:02 PDT
