Respected Experts,
I am trying to perform Pep_GaMD in Amber26 academic version, but from the equilibration phase with the first ntave value, I am getting errors.
Most of them are "of length = 513Failed an illegal memory access was encountered" and occasionally "of length = 513Failed operation not supported on global/shared address space" and "of length = 513Failed unspecified launch failure".
I then talked to Pep_GaMD people. They told me to use ntf=1, which was previously 2. It ran only one time but ended in the middle. Now it won't run a single step and immediately throws " "of length = 513Failed an illegal memory access was encountered".
The system was prepared in CHARMM-GUI and went through several stages of equilibration and a cMD run before submitting to PeP_GaMD. I separated the runs into three parts- ntcmd, nteb and production.
I earnestly request you to kindly take a look at the issues, as a lot of my work depends on it.
I am pasting the nteb step parameters here with some information about the workstation being used for the run.
OS = Ubuntu 22.04.5 LTS
GPU = NVIDIA RTX 6000 Ada Generation
CUDA 12.1 was used to compile Amber26 (pmemd26).
RAM = 256 GB
File Assignments:
| MDIN: 3_6-nteb.mdin
| MDOUT: nteb.mdout
| INPCRD: ntcmd.rst7
| PARM: step5_input.parm7
| RESTRT: nteb.rst7
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: nteb.nc
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
&cntrl
imin=0,
irest=1,
ntx=5,
ntt=3,
gamma_ln=1.0,
tempi=310,
temp0=310,
ig=-1,
cut=9.0,
dt=0.002,
ntc=2, ntf=1,
tol=0.000001,
ntpr=4000,
ntwx= 100000,
ntwr=50000,
ntxo=2, ioutfm=1,
iwrap=1,
barostat=1,
ntp=3,
csurften=3,
ninterface=2,
pres0=1.0,
taup=5,
watnam='WAT',
owtnm='O',
nstlim=16000000,
igamd=15,
iE=1,
iEP=1,
iED=1,
irest_gamd=1,
ntcmdprep=0,
ntcmd=0,
ntebprep=800000,
nteb=16000000,
ntave=400000,
sigma0P=3.0,
sigma0D=6.0,
icfe=1,
ifsc=1,
gti_cpu_output=0,
gti_add_sc=1,
timask1=':399-429',
scmask1=':399-429',
timask2='',
scmask2=''
/
Thank you and regards,
Sincerely,
Suvajit
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Received on Sat Jun 20 2026 - 00:00:02 PDT
