Thanks Jason and Prof. Monard.
One more question. Sometimes I got the results regarding "Infinity".
For example, the results below I got from the .out file (running on GPU
installed in a server, using ALPB Implicit, amber14, ff12SB), as below:
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 223686.99 79.15
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 2049.98 0.73
| RunMD 56857.13 20.12
| Other 0.00 0.00
| ------------------------------
| Total 282594.10
| Generalized Born CPU Time:
|
| Routine Sec %
| ------------------------------------
| Radii Calc 0.00 0.00
| Diagonal Calc 0.00 0.00
| Off Diagonal Calc 0.00 0.00
| GBSA LCPO Calc 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 0 steps:
| Elapsed(s) = 0.03 Per Step(ms) = +Infinity
| ns/day = 0.00 seconds/ns = +Infinity
|
| Average timings for all steps:
| Elapsed(s) = 283573.63 Per Step(ms) = 5.67
| ns/day = 30.47 seconds/ns = 2835.74
| -----------------------------------------------------
| Setup CPU time: 0.62 seconds
| NonSetup CPU time: 282594.10 seconds
| Total CPU time: 282594.72 seconds 78.50 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 283573 seconds
| Total wall time: 283574 seconds 78.77 hours
Is it normal or unexpected when it shows "Infinity"? Other results show
some values instead of "Infinity" though.
However, I checked the system (energy, density, conformation, etc.) and all
are reasonable.
Im wondering what effect it may bring if it shows "Infinity"?
Thank you.
Chinh
On Thu, Jun 4, 2015 at 8:51 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jun 4, 2015 at 8:35 AM, Patrick McGrath <ptmcgrat.gmail.com>
> wrote:
>
> > Hi Jason,
> >
> > Would this cutoff also appropriate for membrane simulations?
> >
>
> ​Depends on who you ask and what membrane force field you're using. If
> you're using the CHARMM force field, they'll tell you that you need a 12 A
> cutoff and ideally a vdW force-switch turned on at 10 A (which Amber
> doesn't have).
>
> The Lipid14 paper uses a 10 A cutoff, so I would suggest using that for
> Lipid14 simulations. The long-range dispersion correction assumes
> isotropic particle distribution, and membranes are anisotropic systems. As
> a result, the correction is less accurate for lipid simulations, so a
> larger cutoff is probably justified.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 04 2015 - 19:00:03 PDT
