Hi Suvajit,
Normally the issue you mentioned could be resolved by more “thorough” energy minimization and equilibration of your simulation starting structure. But the way your prepared your simulation input files (involving GROMACS and file conversions) could complicate the problem.
I would recommend using simulation input files shared with our recent publications, you can test and see how the input parameters are set and systems are prepared (check out the method details in the paper), e.g.: https://pubs.acs.org/doi/10.1021/acs.jpcb.5c05305, with simulation input files for the Pep-GaMD simulations in the public repository Figshare: 10.6084/m9.figshare.29691206<https://doi.org/10.6084/m9.figshare.29691206>, 10.6084/m9.figshare.29689628<https://doi.org/10.6084/m9.figshare.29689628>, 10.6084/m9.figshare.29682797<https://doi.org/10.6084/m9.figshare.29682797>, 10.6084/m9.figshare.29682371<https://doi.org/10.6084/m9.figshare.29682371>.
Hope this helps,
Yinglong
Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology
Computational Medicine Program
Lineberger Comprehensive Cancer Center
University of North Carolina - Chapel Hill
http://miaolab.org<
http://miaolab.org/>
Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov
On Jun 20, 2026, at 3:00 PM, amber-request.ambermd.org wrote:
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Today's Topics:
1. Help with GaMD: Illegal Memmory Access Error (Suvajit Das)
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Message: 1
Date: Sat, 20 Jun 2026 06:34:50 +0000
From: Suvajit Das <suvajit.das.jcbose.ac.in>
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: [AMBER] Help with GaMD: Illegal Memmory Access Error
Message-ID:
<PN2PR01MB8979AA4629AA9F60A76D0912D3E12.PN2PR01MB8979.INDPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
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 Mon Jun 22 2026 - 11:30:02 PDT
