Hi, Yao Li
You cannot run with just ONE image, the string method only applies when you
use multiple images.
Feng
On Sat, Mar 16, 2019 at 9:39 AM 李耀 <liyao17.mails.tsinghua.edu.cn> wrote:
> Dear Amber users,
>
>
> I'm running Swarms-of-trajectories String Method in Amber 18, and these
> are a pair of example of my input files and cv files:
>
>
> mdin.001:
> &cntrl
> imin=0, ntx=1, irest=0, ntxo=1, ntc=2, ntf=2, nstlim=10000,
> ntt=3, gamma_ln=2.0, temp0=300.0, ntpr=10, ntwr=10, ntwx=10,
> dt=0.002, ig=-1, ntb=1,ntr=0, cut=10.0, ioutfm=1,
> iwrap=1,infe=1,
> /
>
>
> &stsm
> image = 1
> repeats = 20
> equilibration = 980
> release = 20
> smoothing = 0.06
> report_centers = 'ALL'
>
>
> output_file = 'stsm.001.txt'
> output_freq = 10
> cv_file = 'cv.1'
> /
> cv.1:
> &colvar
> cv_type = 'TORSION'
> cv_ni = 4, cv_i = 5653, 5639, 5620, 5551
> anchor_position = 0.5235
> anchor_strength = 20.0
> /
>
>
> &colvar
> cv_type = 'TORSION'
> cv_ni = 4, cv_i = 5541, 5649, 5653, 3386
> anchor_position = 1.5705
> anchor_strength = 20.0
> /
>
>
> The command is: nohup /software/amber18/bin/pmemd.cuda -O -i mdin.001 -p
> new_mono.prmtop -c inpcrd.001 -o test1.out -x test1.nc -r test1.restrt
> -inf test1.info & . And it came out the following error:
>
>
> Program received signal SIGFPE: Floating-point exception - erroneous
> arithmetic operation.
>
>
> Backtrace for this error:
> #0 0x7FCB8B688E08
> #1 0x7FCB8B687F90
> #2 0x7FCB8AA374AF
> #3 0x6AE5A1 in __nfe_stsm_mod_MOD_on_pmemd_init
> #4 0x677A84 in __nfe_setup_mod_MOD_on_pmemd_init
> #5 0x4B56DB in MAIN__ at pmemd.F90:?
>
>
> When I set infe to 0 to turn stsm down, it works well. I couldn't figure
> out what the problem is. Have you met similar situations before? What
> should I do about this?
>
>
> Thank you!
>
>
> Best,
> Yao Li
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>
--
Feng Pan
PostDoc
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Sun Mar 17 2019 - 22:00:02 PDT
