Re: rule of thumb for dcd sampling frequency?

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Mar 22 2011 - 04:47:29 CDT

Richard,

Axel, as always, give best explanation

Branko

On 3/22/2011 12:43 AM, Richard Wood wrote:
> Wouldn't saving every picosecond be adequate?
>
> Richard
>
> ------------------------------------------------------------------------
> *From:* Branko <bdrakuli_at_chem.bg.ac.rs>
> *To:* Irene Newhouse <einew_at_hotmail.com>; namd-l <namd-l_at_ks.uiuc.edu>
> *Sent:* Mon, March 21, 2011 2:13:51 PM
> *Subject:* Re: namd-l: rule of thumb for dcd sampling frequency?
>
> Irene,
>
> This strongly depend on what you planed to do with your output - i.e
> which type of analysis you want to do on your output. The best way to
> find most suitable sampling is to find how other sampled their systems
> looking on elements common to analysis of their systems and that which
> you planed At first 100 ns is very long, so maybe better to divide
> your simulation on phases - if you apply any biasing method carefully
> read NAMD ug before this. Second point is size of your system -
> contribute to the size of trajectory, especially if system is big and
> trajectory long. So according to my knowledge, the best way is to look
> on already published references and compare with your system and your
> need. God point to begin is:
> http://www.ks.uiuc.edu/Research/namd/papers.html#cites, providing that
> you are already skilled in setting-up simulation and in analysis of
> output, in this respect the good way is to pass NAMD tutorials that
> can be found on the NAMD main web-page
> (http://www.ks.uiuc.edu/Research/namd/)
>
> Branko
>
> On 3/21/2011 7:26 PM, Irene Newhouse wrote:
>> What are some rules of thumb for trajectory sampling? For instance,
>> if you're intending to simulate for 100nsec, how many frames sample
>> the time span adequately? 1 microsec? Pointers to references would be
>> greatly appreciated.
>>
>> Thanks!
>> Irene Newhouse
>>
>>
>>
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