AMBER Archive (2007)

Subject: Re: AMBER: Implicit solvent simulation is too slow.

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 10 2007 - 08:07:50 CDT

the same simulation meaning also in implicit solvent?
Amber is not optimized for implicit solvent simulations with cutoff.
it has been discussed many times on this list that PME simulations for
large systems are often faster than GB simulations. Check the archives.

we might be able to help more if you tell us which program you
are using (sander, pmemd, other)

On 8/10/07, SeungPyo Hong <sp1020_at_gmail.com> wrote:
> Dear amber users,
> Go to the point, I found my Implicit solvent calculation is too slow.
> Could anybody tell me whether my simulation is problematic or Amber itself
> is slower than I had expected?
>
> It tooks about 28.3 hours for 1ns simulation under following condition:
>
> 28.3 hours / 1ns simulation
> 16 Xeon DP 2.8 GHz CPUs
> 4107 atoms (288 residues protein + 1 ligand)
> implicit solvent simulation
>
> The run option of the MD is this:
> 1 Equilibration Molecular Dynamics: name (Implicit Solvent Model)
> 2 &cntrl
> 3 nstlim = 50000, dt = 0.002,
> 4 tempi = 300.0, temp0 = 300.0,
> 5 ntpr = 100, ntwx = 100, ntwr = 1000,
> 6 imin = 0, irest = 1, ntx = 7,
> 7 ntb = 0,
> 8 taup = 2.0,
> 9 cut = 10,
> 10 ntr = 0,
> 11 ntc = 2, ntf = 2,
> 12 igb = 1,
> 13 ntt = 3, gamma_ln = 1.0
> 14 /
>
> I didn't run explicit solvent simulation yet. (It is waiting its turn in the
> queue...)
> But the same simulation done with GROMACS tell me it tooks about 15.4 hour s
> for 1ns simulation.
>
> --
> --------------------------------------------------
> 'God used beautiful mathematics in creating the world.'
> -Paul Dirac
> 'But he created too many object.'
> -Seungpyo Hong
>
> Seungpyo Hong
> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
> Tel. (82)-18-372-2468
> sphong__at_kaist.ac.kr
> sp1020_at_gmail.com
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