[gmx-users] Poor exchange probability for REMD

[David van der Spoel]

On 2011-11-20 03:03, ÏéÇ« ¿× wrote:
> Dear Mark,
>    Thanks for your prompt reply!
>> Pre-equilibration at the right temperature is always a good
>> idea, not just for REMD.
>
>    Right temperature? I guess you mean pre-equilibrate at every replica temperatures, do you think so?
>
>> However for NVT REMD you need to
>> equilibrate the other temperatures at the same box size that
>> is sound for the temperature at which you want to make
>> observations.
>
>    If i am interested in the properties at 3OOK, i may equilibrate the system at 300K with NPT ensemble, then equilibrate system at every replica temperatures with the same box size obtained from the NPT simulation at 300K.Is it right?
>
Why would you want to simulate at high pressure and high temperature? 
Your proteins will unfold even faster. NVT REMD means your replicas 
above 300 K will have too high P, at 360 K close to 1000 bar. Check 
http://folding.bmc.uu.se/remd/index.php if you need to choose T for 
REMD. The paper that describes the algorithm was published here: 
http://dx.doi.org/10.1039/b716554d

>> Even given that, there is no strong reason to suppose that
>> a temperature distribution following a simple mathematical
>> formula should lead to equal exchange probabilities on a
>> "real" system with free energy bottlenecks. Knowing that one
>> might need to be adding more replicas at relevant
>> temperatures is something that can only be determined
>> empirically - and probably from more than 2ns.
>
>     Yes, that's right! While the exchange probabilities were unequal for neighboring temperatures and maybe very high (0.3~0.4), i think i should remove some replicas at which the exchange probabilities were higher and add some replicas to increase the upper limit of the temperature range for REMD.
>     Meanwhile, anther question, what's the proper range for the exchange probability?  Does the high exchange probability impair the properties we want to observe or just a waste of computational resources?
>     Best regards!
>     Xiangqian Kong
>
>
> --- On Sat, 11/19/11, Mark Abraham<Mark.Abraham at anu.edu.au>  wrote:
>
>> From: Mark Abraham<Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] Poor exchange probability for REMD
>> To: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
>> Date: Saturday, November 19, 2011, 12:14 AM
>> On 18/11/2011 12:43 PM, ÏéÇ« ¿×
>> wrote:
>>> Dear GMX users，
>>>       Recently i am performing the
>> REMD simulation with Gromacs program and the temperature
>> distribution for each replica was predicted with the server
>> "http://folding.bmc.uu.se/remd/". However, after a 2-ns
>> short test simulation with 64 replicas  , i checked the
>> exchange probability for the neighboring replicas and find
>> the exchange probability was about 0.3 to 0.4 (as the file i
>> attached )but the desired probability was 0.2. Meanwhile, i
>> found the exchange probabilities fluctuated markedly for
>> each pair of  replicas while ideally we may hope they
>> were consistent with each other.  I don't know whether
>> this is acceptable or must be fixed up, or  a longer
>> simulation time and pre-equilibrium at different replica
>> temperature for each replica was needed.
>>
>> Pre-equilibration at the right temperature is always a good
>> idea, not just for REMD. However for NVT REMD you need to
>> equilibrate the other temperatures at the same box size that
>> is sound for the temperature at which you want to make
>> observations.
>>
>> Even given that, there is no strong reason to suppose that
>> a temperature distribution following a simple mathematical
>> formula should lead to equal exchange probabilities on a
>> "real" system with free energy bottlenecks. Knowing that one
>> might need to be adding more replicas at relevant
>> temperatures is something that can only be determined
>> empirically - and probably from more than 2ns.
>>
>> Mark
>>
>>>        The system i simulated
>> includes 60074 atoms which consists of 155 residues,19173
>> waters and 14 chloridions. I first equilibrium the system
>> for 2ns with NPT ensemble at 300K, then start the REMD
>> simulation for 64 different replicas (temperature ranges
>> from 300 to 386K) with NVT ensemble and the exchange attempt
>> time was 2-ps(1000 integral steps).
>>>        Now i was totally puzzled and
>> don't know how to figure out these problems,i am eager for
>> the help from you and any suggestions will be greatly
>> appreciated!
>>>        Best regards!
>>>        Xiangqian Kong
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se