I haven't written more often than each ps in years except like
Dave says for special purposes. Lately we often write at 10ps intervals
for long simulations since the longer the runs are the less we are
usually interested in ps resolution. The structures just aren't very
different,
though that is useful when making movies to show the dynamics.
carlos
Robert Duke wrote:
> Dave -
> I think I based this on some discussion on the either the dev or the
> users list; I don't remember if you were involved, but it was some of
> the guys I considered more experienced in the practical aspects; I
> mostly do code. So it is folklore without analysis, but it was amber
> folklore (I think the statement was something to the effect that it is
> good to have 0.25 psec snapshots). Sorry if I have been propagating
> something that is not quite right based on faith. Anybody else want
> to weigh in on this issue? It is actually really impt in terms of the
> cost of simulation and how far you can scale (bigger traj are a pain,
> and have a real cost at high scaling, and as the systems get bigger
> the cost goes up).
> Regards - Bob
>
> ----- Original Message ----- From: "David A. Case" <case.scripps.edu>
> To: <amber-developers.scripps.edu>
> Sent: Thursday, May 04, 2006 6:39 PM
> Subject: Re: amber-developers: Troubles at PSC
>
>
>> On Thu, May 04, 2006, Robert Duke wrote:
>>
>>> I dump trajectory every 250 steps
>>
>>
>> Is this a real requirement, i.e. do you need sub-picosecond
>> resolution in
>> dynamics? The structures at this time resolution will be highly
>> correlated
>> with each other, so there is in effect redundant information in the
>> snapshots.
>>
>> I haven't saved snapshots at less than 1 ps resolution (usually 2ps
>> or longer)
>> for a long time. In the cases where I need more fine grained
>> information, I
>> usually run a short, "fine-grained" simulation (with a small ntwx) to
>> get the
>> needed data.
>>
>> It should be clear that I may be way off base here, since I don't
>> know the
>> real requirements. But you might want to see if you could refine the
>> requirements to require less frequent disk access.
>>
>> ....regards...dave
>>
>>
>
Received on Fri May 05 2006 - 08:13:57 PDT
