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
_______________________________________________
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 Tue Jun 10 2014 - 12:30:03 PDT
