Re: [gmx-users] Question about 'mdrun -nosum'

[Mark Abraham]

On Fri, Dec 14, 2012 at 3:46 PM, Thomas Schlesier wrote:

> Dear all,
> i have a small question regarding the '-nosum' option of 'mdrun'.
> The manual states:
>
> For a global thermostat and/or barostat the temperature and/or pressure
> will also only be updated every nstlist steps. With this option the energy
> file will not contain averages and fluctuations over all integration steps.
>
> Second sentence is clear to me. But the first sentence give me some
> thoughts.
> I think this would introduce some errors, but what is about the magnitude
> of these?
>

Indeed, that does introduce a new approximation, but as you and Dawei said
it's probably drowned out in the noise. Constant point charges are not a
very good model for much...

There is work going on to try to make it easier to quantify these kinds of
(non-)effects, e.g. http://arxiv.org/abs/1208.0910

Mark

I would expected that the errors are in the same order of the errors in the
> forces due to the neighborlist search (error due to the fact that one uses
> 'nstlist=5' instead of 'nstlist=1') and would be more or less negilegible,
> if one doesn't use a very larger 'nstlist'-value.
>
> But to be on the save side i wanted to ask.
>
> Greetings
> Thomas
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Re: [gmx-users] Question about 'mdrun -nosum'

[Da-Wei Li]

I think the same way as you. They do bring in errors but this is acceptable
in normal MD because we already have lots of approximations. BTW, -sum has
been dropped from 4.5, in other words, Gromacs won't calculate global
Energy every step by default now.

dawei


On Fri, Dec 14, 2012 at 9:46 AM, Thomas Schlesier wrote:

> Dear all,
> i have a small question regarding the '-nosum' option of 'mdrun'.
> The manual states:
>
> For a global thermostat and/or barostat the temperature and/or pressure
> will also only be updated every nstlist steps. With this option the energy
> file will not contain averages and fluctuations over all integration steps.
>
> Second sentence is clear to me. But the first sentence give me some
> thoughts.
> I think this would introduce some errors, but what is about the magnitude
> of these?
> I would expected that the errors are in the same order of the errors in
> the forces due to the neighborlist search (error due to the fact that one
> uses 'nstlist=5' instead of 'nstlist=1') and would be more or less
> negilegible, if one doesn't use a very larger 'nstlist'-value.
>
> But to be on the save side i wanted to ask.
>
> Greetings
> Thomas
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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[gmx-users] Question about 'mdrun -nosum'

[Thomas Schlesier]

Dear all,
i have a small question regarding the '-nosum' option of 'mdrun'.
The manual states:

For a global thermostat and/or barostat the temperature and/or pressure 
will also only be updated every nstlist steps. With this option the 
energy file will not contain averages and fluctuations over all 
integration steps.


Second sentence is clear to me. But the first sentence give me some 
thoughts.
I think this would introduce some errors, but what is about the 
magnitude of these?
I would expected that the errors are in the same order of the errors in 
the forces due to the neighborlist search (error due to the fact that 
one uses 'nstlist=5' instead of 'nstlist=1') and would be more or less 
negilegible, if one doesn't use a very larger 'nstlist'-value.


But to be on the save side i wanted to ask.

Greetings
Thomas
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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