I fiddled around with my .in file and modified the 02_Heat.in file on the AMBER lipid tutorial page. I'll include it below in case other people run into the same issue down the road. I'm still having issues with my system, but it's related to a bond made by tleap and I'll start a new thread for that.
Sam
Lipid 128 heating 100K
&cntrl
imin=0, ! Molecular dynamics
ntx=1, ! Positions read formatted with no initial velocities
irest=0, ! No restart
ntc=2, ! SHAKE on for bonds with hydrogen
ntf=2, ! No force evaluation for bonds with hydrogen
tol=0.0000001, ! SHAKE tolerance
nstlim=25000, ! Number of MD steps
ntt=3, ! Langevin thermostat
gamma_ln=1.0, ! Collision frequency for Langevin thermostat IS 5 in ours
ntr=1, ! Restrain atoms using a harmonic potential
! (See the GROUP input below)
ig=-1, ! Random seed for Langevin thermostat
ntpr=100,
ntwr=10000,
ntwx=100, ! Write to trajectory file every ntwx steps
dt=0.002, ! Timestep (ps)
nmropt=1, ! NMR restraints will be read (See TEMP0 control below)
ntb=1,
ntp=0,
cut=10.0,
ioutfm=1, ! Write a binary (netcdf) trajectory
ntxo=2, ! Write binary restart files
restraintmask=':1-1215', ! Restrain the lipids and the protein
restraint_wt=4.0,
&end
&wt
type='TEMP0', ! Varies the target temperature TEMP0
istep1=0, ! Initial step
istep2=25000, ! Final step
value1=0.0, ! Initial temp0 (K)
value2=310.0 / ! final temp0 (K)
&wt type='END' / ! End of varying conditions
________________________________________
From: Samuel A. Ratliff
Sent: Friday, July 31, 2020 4:14 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Issue heating system in equilibration step
Will give that a go, thanks.
Sam
________________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Friday, July 31, 2020 3:19 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Issue heating system in equilibration step
have you tried the same inputs on the CPU version?
I suggest continuing to simplify the inputs stepswise (no restraints, no
weight changes, no nmropt restraints) and see if you can get it to work,
the focus on the variable that made the difference .
On Fri, Jul 31, 2020 at 3:16 PM Samuel A. Ratliff <Samuel.Ratliff17.kzoo.edu>
wrote:
> I've 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. Otherwise, the results are identical.
>
> Sam Ratliff
> ________________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, July 31, 2020 3:10 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Issue heating system in equilibration step
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 06 2020 - 10:00:03 PDT
