Subject: Re: MD or MC

From: "Arne Eofsson ([email-masked])" <[email-masked]>
Date: Wed, 09 Nov 94 13:56:48 -0800

>Q:
>> 	   Which one, MD or MC, you will select if CPU time-constraint
>>    is imposed ? 
>A:
>> The choice between MD and MC depends not on your CPU time allocation,
>> but on the problem you want to solve. 
>
>There is a class of Monte Carlo simulations which can be directly compared
>with molecular dynamics. These are the MC studies of time-dependent phenomena.
>See for example works on polymer reptation by Kurt Binder or on biopolymers
>by team Skolnick - Kolinski. In such an approach, a new MC configuration is 
>formed from the previous one (after being accepted with Metropolis criterion). 
>This may be assumed to be equivalent to a time evolution of the system. Because
>changes in the system between consecutive MC configurations are greater than
>after a single MD time step, one can treat the MC step as a time period much
>longer than the MD time step. In this way, the time-dependent MC simulations 
>extend longer in time than the MD with the same number of steps, although 
>the exact length of the MC time step is hard to estimate and MC gives only
>positions of the particles, but not the momenta. However, MC may be preferred 
>over MD, if one simulates large systems with long relaxation times which are
>beyond reach of current computers.

I would like to point out some important facts about these type of simulations.
1. A direct comparison is not possible, Skolnick/Kolinski did some comparisons
   between their (lattice) MC simulations with brownian dynamics simulations 
   and claimed that their detailed lattice models where about 2-4 times faster
   (Kolinki, et al 1994, Proteins). However Karplus pointed out that the time
   step used in their brownian dynamics simulations was too long.
   (These are just some few problems that can occur)

2. The dynamics that you do in a MC might be very dependent on the type
   of step you allow. You might favor the formation of helixes over sheets
   and so on.

3. I can do things in a MC simulation that I would never be able to in MD
   (For instance I can get a protein starting from a random conformations
   to be folded into a compact structure under the AMBER potential in a 
   day or two on a workstation). This woud take much longer with MD.
   I haven't tried but I think so.

4. In MC I can use energy functions without being able to take their 
   derivative. (very usefull in some cases)

5. In MC I can put on any constrraints that I want to.

6. Usually for a detailed description (of a protein) and a detailed (amber)
   energy function MD is more accurate (my guess)

arne

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