Date: Fri, 19 Sep 2025 18:32:10 +0530
this is my input file,
equilibrating in NVT
&cntrl
imin=0,
irest=0,
ntx=1,
ntb=1,
ntt=8,gamma_ln=2.0,
tempi=300.0,temp0=300.0,
nstlim=5000,dt=0.00025,
ntpr=5,ntwx=5,ntwr=2000,
ifqnt=1,iwrap=1,ioutfm=1,
cut=12.0,infe=1
/
&qmmm
iqmatoms=
1456, 1457, 1458, 1459, 1460, 1461, 1462, 1463,
1464, 1465, 1466, 1493, 1494, 1495, 1496, 1497,
1498, 1499, 1500, 1501, 1502, 1503, 1840, 1841,
1842, 1843, 1844, 1845, 1846, 1847, 1848, 1849,
1850, 4102, 101, 102, 103, 104, 105, 106,
107, 108, 109, 110, 111, 112, 113, 114,
115, 970, 971, 972, 973, 974, 975, 976,
977, 991, 992, 993, 994, 995, 996, 997,
998, 999, 1000, 1001, 1038, 1039, 1040, 1041,
1042, 1043, 1044, 1045, 1419, 1420, 1421, 1422,
1423, 1424, 1425, 1426, 1427, 1428, 1429, 1625,
1626, 1627, 1628, 1629, 1630, 1631, 1632, 1633,
3067, 3068, 3069, 3070, 3071, 3072, 3073, 3074,
3081, 3082, 3083, 3084, 3085, 3086, 3087, 3088,
4103, 4104, 4105, 7220, 7221, 7222, 11495, 11496,
11497, 14549, 14550, 14551, 15266, 15267, 15268, 16346,
16347, 16348, 21254, 21255, 21256, 21929, 21930, 21931,
22736, 22737, 22738, 25997, 25998, 25999, 26099, 26100,
26101, 28364, 28365, 28366, 29867, 29868, 29869, 32864,
32865, 32866, 35906, 35907, 35908, 39074, 39075, 39076,
46799, 46800, 46801, 48026, 48027, 48028,
qmcharge=1,
qmshake=0,
qm_ewald=0,
qmcut=8.0,
qm_theory='quick',
qmmm_int=1,
/
&quick
method='B3LYP',
basis='6-31G',
/
&smd
output_file = 'smd.txt'
output_freq = 5
cv_file = 'cv.in'
/
this the command
$ambexe -O -i smd_1.in -o smd_1.out -p 2ILI_solv.prmtop -c f1047.ncrst -r
smd_1.ncrst -x smd_1.nc
On Fri, Sep 19, 2025 at 6:28 PM Ramdhan,Peter A <pramdhan1.ufl.edu> wrote:
> Hey Kriti,
>
> Would you be able to show us your input file (amber inputs)? If you are
> using a HPC to run your calculations, can you also show the input you are
> using for that as well (the command you send to the scheduler to run your
> calculation)?
>
> Sincerely,
>
> *Peter Ramdhan, PharmD*
>
> 3rd Year PhD Student
> T32 PARADIGM Postdoctoral Fellow
>
> Dept. of Medicinal Chemistry, Li Lab
> University of Florida College of Pharmacy
>
>
> ------------------------------
> *From:* Kriti Shukla via AMBER <amber.ambermd.org>
> *Sent:* Friday, September 19, 2025 8:52 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] Error in Steered QM/MM MD
>
> [External Email]
>
> I have been trying to perform steered QM/MM MD. I have restarted again from
> the previous SMD file to increase the run time, but this type of error is
> showing after some steps, and the run is halted in between.
> /scratch/slurm_conf/spool/slurm/d/job29046/slurm_script: line 24:
> /home/srabanimd/amber24/amber.sh: Permission denied
> sander.quick.cuda:
>
> /home/testfac5/amber24_src/AmberTools/src/quick/src/cuda/cusolver/quick_cusolver.c:165:
> cuda_diag_: Assertion `CUSOLVER_STATUS_SUCCESS == cusolver_status' failed.
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0 0x7f7ed840651f in ???
> #1 0x7f7ed845aa7c in ???
> #2 0x7f7ed8406475 in ???
> #3 0x7f7ed83ec7f2 in ???
> #4 0x7f7ed83ec71a in ???
> #5 0x7f7ed83fde95 in ???
> #6 0x7f7edd83af32 in ???
> #7 0x7f7edd6a569e in ???
> #8 0x7f7edd6a6c54 in ???
> #9 0x7f7edd7cb7ae in ???
> #10 0x7f7edd6a8de6 in ???
> #11 0x7f7edd6aa316 in ???
> #12 0x7f7edd6ab0a6 in ???
> #13 0x762937 in ???
> #14 0x707540 in ???
> #15 0x5a0ef9 in ???
> #16 0x6332fe in ???
> #17 0x5e75c0 in ???
> #18 0x5e04cf in ???
> #19 0x5e0525 in ???
> #20 0x7f7ed83edd8f in ???
>
> I am unable to understand.
>
>
>
>
> --
> Kriti Shukla
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology, Kharagpur
> India. 721302
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