Hi Ben,
In that case simulation have been crashed just after start of the nvt
heating with the error
| Local SIZE OF NONBOND LIST = 22082443
| TOTAL SIZE OF NONBOND LIST = 22082443
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -223698.7003 EKtot = 0.0000 EPtot =
-223698.7003
BOND = 540.9142 ANGLE = 3101.7570 DIHED =
12264.5560
1-4 NB = 3729.6115 1-4 EEL = 14167.5921 VDWAALS =
27563.5169
EELEC = -285066.6481 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1425E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 0; vmax = 20.2904
vlimit exceeded for step 1; vmax = **********
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 11217 19269 19272
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Might the problem due to the N and C caps added by the tleap?
CHL 34
CLEU 1
NASP 1
OL 136
PA 136
PC 136
WAT 14272
I didn't noticed such caps in case of rhodopsin from tutorial where no such
problem have been occurred.
James
2014-06-10 23:04 GMT+04:00 Benjamin D Madej <bmadej.ucsd.edu>:
> Hi James,
>
> One noticeable thing about your input is that the nstlim and istep2 do not
> match. I would guess that you're heating your system too fast, leading to
> instabilities. It's worth checking the input structure as well for any
> irregularities.
>
> The error you show is a GPU specific error. Only pmemd.cuda could give you
> that error. I would attempt to run the simulation again with just "pmemd"
> and it's likely that you'll get more information about what's going wrong
> with your simulation.
>
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
> SDSC
>
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Tuesday, June 10, 2014 12:05 AM
> To: AMBER Mailing List
> Subject: [AMBER] Equilibration of membrane protein
>
> Dear Amber users!
>
> I've faced with the problem of the initial heating of my protein-membrane
> system in NVT using script from the tutorial (before this stage my protein
> have been properly minimized):
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 9600 -2.0119E+05 7.8407E-01 7.5497E+01 C112 21832
>
> BOND = 16716.8403 ANGLE = 3296.3449 DIHED =
> 12715.8231
> VDWAALS = 25033.9597 EEL = -277016.9354 HBOND =
> 0.0000
> 1-4 VDW = 3857.1824 1-4 EEL = 14205.2856 RESTRAINT =
> 0.0000
>
> the nvt script is
>
> Lipid 128 heating 100K
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> ntc=2,
> ntf=2,
> tol=0.0000001,
> nstlim=50000,
> ntt=3,
> gamma_ln=1.0,
> ntr=1,
> ig=-1,
> ntpr=1000,
> ntwr=1000,
> ntwx=1000,
> dt=0.002,
> nmropt=1,
> ntb=1,
> ntp=0,
> cut=10.0,
> ioutfm=1,
> ntxo=2,
> /
> &wt
> type='TEMP0',
> istep1=0,
> istep2=2500,
> value1=0.0,
> value2=100.0 /
> &wt type='END' /
> Hold lipid and protein fixed
> 10.0
> RES 1 754 # <<< restrains applied both on protein and membrane residues
> END
> END
>
>
> the error (occurred both in pmemd and sander) is
>
> pmemd.cuda -O -i ./in/02_Heat.in -o 02_heat.out -p test.prmtop -c
> 01_Min.rst -r 02_Heat.rst -ref 01_Min.rst -x 02_Heat.nc
> Error: unspecified launch failure launching kernel kClearForces
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
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Received on Tue Jun 10 2014 - 22:30:02 PDT
