Re: StepsPerCycle

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Feb 03 2010 - 10:28:38 CST

Many apologies! I didn't read your email carefully and answered the
wrong question.

I'm not really familiar with the "pairlistspercycle" parameter. My
guess is that this will regenerate the pairlists every 20/2 = 10
steps. Even though 10 is no longer a multiple of 4, the full
electrostatics frequency, NAMD still runs with these parameters.

Regards,
Dave

On Feb 3, 2010, at 10:07 AM, David Hardy wrote:

> Hi Myunggi,
>
> With your stated configuration parameters, the bonded interactions
> are evaluated using a timestep of 1.0 fs, the short-range non-
> bonded interactions are evaluated using a timestep of 2*1.0 = 2.0
> fs, and the long-range electrostatics are evaluated using a
> timestep of 4*1.0 = 4.0 fs.
>
> Regards,
> Dave
>
>
> On Feb 3, 2010, at 9:33 AM, Myunggi Yi wrote:
>
>> Dear NAMD users,
>>
>> I am so confused by the manual about the update of the pair list
>> of non-bonded interactions.
>>
>> If the followings are the simulation parameters, what is the
>> update frequency of the pair list of non-bonded interactions?
>>
>> cutoff 12.
>> switching on
>> switchdist 10.
>> pairlistdist 13.5 # Description: A pair list
>> is generated pairlistsPerCycle times each cycle
>>
>> timestep 1.0
>> rigidBonds all
>> nonbondedFreq 2
>> fullElectFrequency 4
>> stepspercycle 20 # Description: Number of
>> timesteps in each cycle. Each cycle represents the number of
>> timesteps between atom reassignments.
>> pairlistspercycle 2 # Description: Rather than
>> only regenerating the pairlist at the beginning of a cycle,
>> regenerate multiple times in order to better balance the costs of
>> atom migration, pairlist generation, and larger pairlists.
>>
>>
>>
>>
>> Thank you.
>>
>>
>> --
>> Best wishes,
>>
>> Myunggi Yi
>> ==================================
>> 91 Chieftan Way
>> Institute of Molecular Biophysics
>> Florida State University
>> Tallahassee, FL 32306
>>
>> Office: +1-850-645-1334
>>
>> http://sites.google.com/site/myunggi/
>> http://people.sc.fsu.edu/~myunggi/
>>
>
>
>
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois
> dhardy_at_ks.uiuc.edu
> http://www.ks.uiuc.edu/~dhardy/
>
>
>
>

-- 
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/

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