Hello all,
I've been trying to equilibrate a protein embedded in a lipid bilayer and have been having some issues. So far, I've been roughly using the AMBER lipid tutorial at
http://ambermd.org/tutorials/advanced/tutorial16/index.html as a guide. I've been able to minimize the system in three phases, minimizing the waters, then the waters and the lipids, then minimizing the whole system. However, when I attempt to heat the system, pmemd.cuda dumps core with the following message:
*** Error in `pmemd.cuda': double free or corruption (out): 0x000000000448df70 ***
In the heat.out file where AMBER writes its output, the last line is "LOADING THE CONSTRAINED ATOMS AS GROUPS". AMBER also writes a NetCDF trajectory file, but when I view it in VMD, there are no atoms and the size of the NetCDF file is significantly smaller than I expect. I've opened the min_system.rst file that the heating step starts from in VMD and it seems to be fine. I've also been able to minimize the min_system.rst file again, so it doesn't seem like the restart file is the problem. From a conceptual standpoint, I was also unsure if when heating the system, I should restrain only the protein (resids 1-498) or the protein and the lipids (resids 1-1215). I've also tried removing the constraints on the system and it dumps core at the same place, though doesn't print "LOADING THE CONSTRAINED ATOMS AS GROUPS" and instead prints a line of dashes like the file was going to go on to the next section of the output.
Below is my heat.out file. (Note: I know that AMBER16 is not particularly current, but my lab has custom code written for AMBER16 that necessitates its use.) Any suggestions to fix this issue or insights into what is going wrong are welcome. Thanks!
-------------------------------------------------------
Amber 16 PMEMD 2016
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 16
| Run on 07/28/2020 at 12:39:48
| Executable path: pmemd.cuda
| Working directory: /media/furgelab/Store/archive/sam_ratliff/simulations/lipid/1_lipid/2019.08.13_1/eq
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: /home/furgelab/scripts/MD/inputs//heat_lipid.in
| MDOUT: heat/heat.out
| INPCRD: minimization/min_system.rst
| PARM: ../build/system/1_lipid.prmtop
| RESTRT: heat/heat.rst
| REFC: minimization/min_system.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: heat/heat.nc
| MDINFO: heat/heat.mdinfo
| MDFRC: mdfrc
Here is the input file:
Heating up the system equilibration stage 1
&cntrl
imin=0, irest=0,
ntx=1, ig=-1,
nstlim=25000,
dt=0.002,
ntpr=7, ntwr=7, ntwx=7,
tempi=0.0, temp0=310.0,
ntt=3, gamma_ln=5, ntb=1, ntp=0,
ntc=2, ntf=2, nmropt = 1,
cut=9, ntr=1,
restraintmask='(:1-498.CA,C,N)', !was :1-1215
restraint_wt=4.0,
ioutfm=1,
iwrap=1,
&end
&wt TYPE='TEMP0', istep1=0, istep2=125000,
value1=0.0, value2=310.0, /
&wt TYPE='END' /
Note: ig = -1. Setting random seed to 78217 based on wallclock time in
microseconds.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 16.0.0
|
| 02/25/2016
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| Precision model in use:
| [SPFP] - Single Precision Forces, 64-bit Fixed Point
| Accumulation. (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 3
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX 980 Ti
| CUDA Device Global Mem Size: 6078 MB
| CUDA Device Num Multiprocessors: 22
| CUDA Device Core Freq: 1.29 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 53.247
| New format PARM file being parsed.
| Version = 1.000 Date = 08/13/19 Time = 12:46:28
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 69270 NTYPES = 32 NBONH = 52859 MBONA = 16283
NTHETH = 56126 MTHETA = 19684 NPHIH = 94026 MPHIA = 61862
NHPARM = 0 NPARM = 0 NNB = 261952 NRES = 10976
NBONA = 16283 NTHETA = 19684 NPHIA = 61862 NUMBND = 106
NUMANG = 233 NPTRA = 258 NATYP = 63 NPHB = 1
IFBOX = 1 NMXRS = 73 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 21 24 26
| Direct force subcell size = 5.0711 5.0986 5.1183
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 7, ntrx = 1, ntwr = 7
iwrap = 1, ntwx = 7, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 4.00000
Molecular dynamics:
nstlim = 25000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 78217
temp0 = 310.00000, tempi = 0.00000, gamma_ln= 5.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 7
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 106.494 Box Y = 122.367 Box Z = 133.077
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 108 NFFT2 = 128 NFFT3 = 128
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
Thanks,
Sam Ratliff
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Received on Tue Jul 28 2020 - 10:30:02 PDT
