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alwens铁杆木虫 (正式写手)
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使用AMBER做分子动力学模拟应该使用哪种温度耦合算法？
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For temperature regulation we will use the newly introduced (AMBER 8.0) Langevin thermostat (NTT=3) to maintain the temperature of our system at 300 K. This temperature control method uses Langevin dynamics with a collision frequency given by GAMMA_LN. This temperature control method is significantly more efficient at equilibrating the system temperature than the Berendsen temperature coupling scheme (NTT=1) that was the recommended method for older versions of AMBER. The biggest problem with the Berendsen method is that the algorithm simply ensures that the kinetic energy is appropriate for the desired temperature; it does nothing to ensure that he temperature is even over all parts of the molecule. This can lead to the phenomenon of hot solvent, cold solute. To avoid this, elaborate temperature scaling techniques for slowly heating the molecule over the course of the simulation were recommended. The Langevin system is much more efficient, however, at equilibrating the temperature and is now the recommended choice for equilibrating temperature in AMBER 8.0. Use the Langevin temperature regulation scheme with care, however, since while it will allow you to equilibrate the temperature of you system efficiently it will alter the fast dynamics of your system. As such, especially with explicit solvent dynamics, it is often better to equilibrate your system using ntt=3 and then, once equilibrated, switch to ntt=1 or alternatively pure Newtonian dynamics (ntt=0). 所以，最终的结论是：升温和平衡部分使用Langevin算法(NTT=3)，而在正式的模拟轨迹中使用Berendsen算法(NTT=1)或者干脆不加耦合(NTT=0)。 |
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3楼2007-12-12 22:41:15
alwens
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More about NTT=3 (zz from amber mailist)
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I know it is quite an involved issue but if this is really the opinion of the AMBER developers then it might be prudent to add a remark to this effect in the "DNA polyA-polyT Decamer" tutorial. This is a really nice tutorial and I believe that most new users will use this to get a feel for what is sensible to do with AMBER. However, my reading of this tutorial left me with quite a different impression regarding ntt=3 and explicit water: Specifically, the following text threw me off the track a bit. From: (http://amber.scripps.edu/tutoria ... minandmd3.html#5.1) 5.1.5) Molecular Dynamics (heating) with restraints on the solute "...Prior to AMBER 8 the recommended method for maintaining temperature was to use the Berendsen thermostat (NTT=1). This method is not very efficient at ensuring the temperature remains even across the system and so one would typically have to use NMR restraints in order to ensure that the heating occurred very gradually over a timescale of about 20 ps. This was essential in order to avoid problems with hot solvent cold solute etc. AMBER 8 now supports the new Langevin temperature equilibration scheme (NTT=3) which is significantly better at maintaining and equalising the system temperature." Note that this is in the context of equilibrating in explicit solvent. NTT=3 is also used in the production example of A-DNA. Please don't take this mail the wrong way but it seems to me that beginners and semi-experienced users alike could take the information in this tutorial to mean that NTT=3 is a good idea in explicit solvent. If it really isn't then it may be helpful to add a comment in the tutorial. Just my $0.02. David. You have hit upon a very hot topic here. Originally when I wrote the DNA tutorial the langevin dynamics temperature regulation was fairly new and not much was known about its behaviour. It was known, however, that overall temperature equilibration was better. However, since then we have become much more familiar with the method and the implications of using it. Essentially while ntt=3 equilibrates your temperature better as a method of maintaining an equilibrium temperature it is probably not so good. This is what Dave was referring to when he was talking about using it with explicit solvent. Essentially it would appear that the best approach, in terms of obtaining accurate dynamics, would be to equilibrate your system initially with ntt=3, since it equilibrates temperature very well, and then, in my opinion, switch to ntt=1 for the production phase. Alternatively assuming your system is well equilibrated you should be able to switch off the thermostat all together (ntt=0) and just run your explicit solvent simulation with no thermostat. This is true since the force field is conservative, hence you should be able to maintain constant energy for a very long time. However, errors in the integrator (the fact you make a timestep approximation) and errors involved with using a cutoff will eventually lead to you bleeding energy over time. Hence I believe a weak thermostat is always a good idea as it corrects for these errors... Anyway, back to the point at hand... Ntt=3. The problems with using ntt=3 in a production calculation, is that it alters the dynamics of your system, essentially the short term dynamics (fast dynamics) are radically altered and so if you are interested in obtaining information about the fast dynamics of your system during the production phase you cannot use ntt=3 since it essentially corrupts this information. Berendsen (ntt=1) does not do this. In terms of the long term dynamics ntt=3 also effects these but where such transitions are not directly dependent on the fast dynamics, i.e. something like the A-DNA to B-DNA conversion, then ntt=3 can actually serve to increase the speed of these dynamics. In other words you can cover more phase space in less time. However, the langevin dynamics while not effecting the actual transition does effect the speed of the transition and as such if you want information regarding timescales of structural interconversions you again need to use ntt=1. Hence if you are just interested in going from a high energy structure to a lower one quickly ntt=3 is probably the best method, but if you want to compute things like time correlation functions then you need accurate fast dynamical information so you need avoid ntt=3. However, in the case of the DNA tutorial it was fortuitous in the use of ntt=3 since it allows the A-DNA to B-DNA conversion to occur much more quickly than it would using a berendsen thermostat (or none at all). Essentially the langevin dynamics allowed the energy barrier to be crossed much quicker by increasing the sampling of higher energy configurations. Hence for the A-DNA to B-DNA test case it was probably the correct choice. However, this does not mean it would be the correct choice for all explicit solvent simulations... Hence what I will probably do is simply add a few sentences discussing the above to the tutorial to try to make the situation clearer. I hope it makes sense, please let me know if what I have stated makes sense to you, or if it sounds like complete gibberish... Anyway, if it is clear let me know as I will then adjust the tutorial to match. All the best Ross |
2楼2007-12-12 13:52:48