[gmx-users] Temperature interval in REMD simulations

[Florent Hédin]

Dear Ishrat, and dear other gmx-users

I once used the following website, which can help you generating a
temperature set for REMD simulations

http://folding.bmc.uu.se/remd/

It is may be the tool you already used for generating you 18
temperatures, by the way. By trying different values for the 'exchange
probability' field you can change the number of temperatures.

It depends on the system size and the number of water molecules of
course, but try with a larger exchange probability, 0.3 0.4 or 0.5
should increase your number of replica.

Regards,

Florent Hédin

On 19/08/16 12:12, asaffarhi at post.tau.ac.il wrote:
> Dear Ishrat,
> 
> Roughly speaking, the temperatures should be chosen so the acceptance
> rates between replicas in adjacent temperatures are kept relatively
> constant. The high temperature should be such that k_B*T_high should be
> similar to the energy barriers relative to the "equilibrium state". From
> T_high and up your results should not change.
> 
> You can take a look at the last paragraph in the appendix of
> http://www.sciencedirect.com/science/article/pii/S0378437113006468
> 
> In addition there is also Hamiltonian REMD (H-REMD) in which the
> temperature is kept constant and lambda is used instead (not having to
> worry about the speed of the atoms at high temperatures).
> 
> See for example
> https://arxiv.org/pdf/1310.2112v17.pdf, Sec. VI
> 
> There are references in both links.
> 
> Best,
> Asaf
> 
> Quoting ISHRAT JAHAN <jishrat17 at gmail.com>:
> 
>> Dear all
>>
>> I am trying to perform REMD simulation of small peptide. I am doing REMD
>> first time. I am not sure how to decide the temperature interval in a
>> given
>> range. I have used temperature generator for REMD-simulations for 290
>> K to
>>  500 K with exchange probability of 0.25. It gives 18 replicas. However I
>> am repeating the work done by Zachary et al. I am giving the link here.
>> http://www.ncbi.nlm.nih.gov/pubmed/25691742
>>
>>
>> There are 62 replicas generated with temperature range of 290 to 500 K.
>>
>> Can anyone tell me how to generate 62 replica with temperature range
>> of 290
>> to 500 K and also tell how to decide the temperature interval for doing
>> REMD.
>> How temperature is related to the number of replicas.
>>
>>
>>
>> Thanks in Advance
>> -- 
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> 
> 

-- 
Florent Hédin
work at fhedin.com <mailto:work at fhedin.com>
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