I would suggest a short test without the restraint, and if that works to
adjust your restraintmask. I am not sure the parentheses after quotes are
allowed.
On Tue, Jul 28, 2020 at 1:05 PM Samuel A. Ratliff <Samuel.Ratliff17.kzoo.edu>
wrote:
> 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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>
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Received on Fri Jul 31 2020 - 12:30:02 PDT
