Re: [gmx-users] REMD - low temperature ranges

2012-04-27 Thread Krzysztof Kuczera 
If you are only interested in conformational sampling, then it makes 
sense to start at 300 K or even higher - maybe 320 K. The main reason 
for working at lower temperatures is if your system
is unstable - eg. if you expect that the molecule will be mostly 
unfolded at 300 K and you want to sample the folded state. Another 
reason might be having experimental data at lower T, but this
is problematic, as it is hard to model temperature-dependent properties 
with simple force fields.


Krzysztof Kuczera

On 4/27/12 10:06 AM, Tomek Wlodarski wrote:

Hi Mark,

Thanks for reply.

The problem is that I have never found in the papers reasoning behind 
the the lower than 300K temperatures.

Moreover, authors were interested in properties in 300K or above.
I was wondering if this is not based on experience that REMD 
implemented in gromacs works better when you also include lower 
temperature.?

best!

tomek

On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham > wrote:


On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:

Hi,

I have notice that quite often people in REMD simulation use
replicas in lower than 300K temp.
Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources and I am wondering if
for studing 175 aa protein is better to start from 250K and up
to 350 K or choose from 300-400K (just an example)


Depends on the temperature(s) at which you wish to make
observations. Sampling is normally enhanced at higher
temperatures, so unless you want the ensemble at some low
temperatures, it is normal to start at your lowest observation
temperature.

Of course, you could always read the reasoning provided by the
authors in their paper, or email them for clarification...

Mark
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Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
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Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html


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Re: [gmx-users] REMD - low temperature ranges

2012-04-27 Thread Tomek Wlodarski 
Hi Mark,

Thanks for reply.

The problem is that I have never found in the papers reasoning behind the
the lower than 300K temperatures.
Moreover, authors were interested in properties in 300K or above.
I was wondering if this is not based on experience that REMD implemented in
gromacs works better when you also include lower temperature.?
best!

tomek

On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham wrote:

> On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:
>
>> Hi,
>>
>> I have notice that quite often people in REMD simulation use replicas in
>> lower than 300K temp.
>> Using for example temperature ranges from 250 to 450K
>> I am wondering what is the purpose of those replicas.
>> I have limited computational resources and I am wondering if for studing
>> 175 aa protein is better to start from 250K and up to 350 K or choose from
>> 300-400K (just an example)
>>
>>
> Depends on the temperature(s) at which you wish to make observations.
> Sampling is normally enhanced at higher temperatures, so unless you want
> the ensemble at some low temperatures, it is normal to start at your lowest
> observation temperature.
>
> Of course, you could always read the reasoning provided by the authors in
> their paper, or email them for clarification...
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] REMD - low temperature ranges

2012-04-27 Thread Mark Abraham 

On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:

Hi,

I have notice that quite often people in REMD simulation use replicas 
in lower than 300K temp.

Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources and I am wondering if for 
studing 175 aa protein is better to start from 250K and up to 350 K or 
choose from 300-400K (just an example)




Depends on the temperature(s) at which you wish to make observations. 
Sampling is normally enhanced at higher temperatures, so unless you want 
the ensemble at some low temperatures, it is normal to start at your 
lowest observation temperature.


Of course, you could always read the reasoning provided by the authors 
in their paper, or email them for clarification...


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] REMD - low temperature ranges

2012-04-27 Thread Tomek Wlodarski 
Hi,

I have notice that quite often people in REMD simulation use replicas in
lower than 300K temp.
Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources and I am wondering if for studing
175 aa protein is better to start from 250K and up to 350 K or choose from
300-400K (just an example)
Thanks!
Best!

tomek
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