[AMBER] »Ø¸´: AMBER TI calculations

From: Huang ZiJian via AMBER <amber.ambermd.org>
Date: Mon, 16 Dec 2024 12:43:16 +0000

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 16 2024 - 05:00:02 PST
Custom Search