Re: many short runs or one long run?

From: Aaron Oakley (oakley_at_rsc.anu.edu.au)
Date: Mon Jul 10 2006 - 21:17:19 CDT

I recommend that you see:
Caves LSD, Evanseck JD, Karplus M. Locally accessible conformations of
proteins: multiple molecular dynamics simulations of crambin. Prot Sci
1998;7:649666. 41.

a++

> 2006/7/10, Ching Wong <wongcw_at_titan.sfasu.edu>:
>> Hi, all.
>>
>> From your experience, do you think it is better to run many shorter
>> run
>> or just one longer run (such as four 2ns runs vs. one 8ns run)?
>>
>> And do you get the exact same result (trajectory, RMSD, RMSF, etc)
>> from
>> a repeated run (same seed)? Is the MD repeatable at all in NAMD?
>> I thought I saw it somewhere in the manual that results may differ.
>> Can someone confirm that, I just want to make sure. :)
>>
>> If the result is not reproducible, what would you say? How can we
>> claim
>> the MD simulation experiment is still reliable???? Any ideas please?
>>
>> Sincerely yours,
>> Jas
>>
>>
>>
>>
>>
>> Quote from Manual
>> seed random number seed
>> Acceptable Values: positive integer
>> Default Value: pseudo-random value based on current UNIX clock time
>> Description: Number used to seed the random number generator if
>> temperature or langevin is selected. This can be used so that
>> consecutive simulations produce the same results. If no value is
>> specified, NAMD will choose a pseudo-random value based on the current
>> UNIX clock time. The random number seed will be output during the
>> simulation startup so that its value is known and can be reused for
>> subsequent simulations. Note that if Langevin dynamics are used in a
>> parallel simulation (i.e., a simulation using more than one processor)
>> even using the same seed will not guarantee reproducible results.
>>
>> -------
>> Jasmine
>>
>
>
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