Hi Vero,
Solvating and equilibrating your ligand in a larger box can solve this issue.
Best regards,
Zijian
________________________________
·¢¼þÈË: VERONICA MARTIN HERNANDEZ via AMBER <amber.ambermd.org>
·¢ËÍʱ¼ä: 2024Äê12ÔÂ16ÈÕ 17:58
ÊÕ¼þÈË: AMBER Mailing List <amber.ambermd.org>
Ö÷Ìâ: [AMBER] AMBER TI calculations
Hi everyone
I'm performing TI calculations and I've got the following error in the ligands_solvated part:
Small box detected, with <= 2 cells in one or more
dimensions. The current GPU code has been deemed
unsafe for these situations. Please alter the
cutoff to increase the number of hash cells, make
use of the CPU code, or (if absolutely necessary)
run pmemd.cuda with the -AllowSmallBox flag. This
behavior will be corrected in a forthcoming patch.
Is safe to use the flag -AllowSamllBox? In my input file I don't have any cutoff and I don't know how this work in this type of calculations
Thanks in advance and best regards
Vero
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Received on Mon Dec 16 2024 - 05:00:02 PST