AMBER Archive (2004)

Subject: Re: AMBER: performance of periodic vs. non-periodic simulation

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Thu May 13 2004 - 11:14:08 CDT

Hi Ben,

thanks very much for this hint!

I think I will try sander_classic of the amber6 distribution that we
have. May be this helps with getting rid of the large fluctuations when
using a cap and a non-infinite cutoff ...

Best,
Oliver

Ben Cossins wrote:
> Hey Oliver,
> I have done a similar thing with amber 7. I found the same large
> fluctuations. In the end i found that this was due to amber 7 using a atom
> based cut off for non-periodic conditions. This meant that charges on
> residues where split across the cut off causing the instabilities. To get a
> residue based cut off for non-periodic conditions you have to go back to
> amber 5.
>
> Hope that helps.
>
> On Wednesday 12 May 2004 8:08 pm, Oliver Hucke wrote:
>
>>Dear Amber users/developers,
>>
>>I am have tried to speed up my simulations by switching from a periodic
>>system with PME to a non-periodic system with a cap of ~300 water
>>molecules on a ligand binding site. My goal is to calculate relative
>>ligand binding energies with MM-PBSA and TI.
>>
>>I first used a non bonded cutoff of 12A for the non-periodic system.
>>This lead to fluctuations of ~1000 to 2000 kcal/mol of the electrostatic
>>energy (corresponding to 10% of the total energy) preventing equilibration.
>>Using a cutoff larger than my system and switching off the update of the
>>non-bonded pairlist solved this problem - but now the simulations are
>>significantly slower than for the periodic system (details below).
>>Is this to be expected?
>>Do I miss something that could speed up the simulations with the cap
>>without leading to instability of the electrostatic energy?
>>
>>Some more details:
>>
>>I am using sander of AMBER8.
>>
>>Periodic system:
>> size: 50000 atoms, truncated octahedron, cut=8A
>> performance: 80ps/day (with dt=0.002)
>>
>>non-periodic system:
>> size: 10000 atoms
>> performance: 30ps/day (dt=0.002)
>>
>>The input for the non-periodic simulation (heating after energy
>>minimization):
>>
>>md, warm belly to 300K
>> &cntrl
>> imin = 0, irest = 0, ntx = 1,
>> nstlim = 20000, dt = .002,
>> ntpr=100, ntwx=5000,
>> ntt = 1, tempi=10.0, temp0 = 300.0, tautp=1.0,
>> ntc = 2, ntf = 2,
>> cut = 999., nsnb=999999, scee = 1.2,
>> ntb = 0,
>> ibelly = 1, ntr = 1,
>> &end
>> &ewald
>> eedmeth=4,
>> &end
>> -- restraint = belly
>>5.0
>> RES a z
>>END
>>END
>> -- belly
>> RES a z
>>END
>>END
>>
>>-----
>>
>>Best regards,
>>Oliver
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
_______________________________________________________________

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu