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[求助]
MS Forcite 模拟高温下大分子在薄膜表面的脱付
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MD新手求助 最近在用MS forcite做MD, 想模拟在加热条件下大分子在炭薄膜表面的脱付作用，但是遇到一些问题。 我的体系是这样的： 周期性结构， 一层是无序碳薄膜（2nm左右厚）， 二层是40 个polymer大分子（分子量2000左右的，~1nm）， 然后是足够厚的真空层。 forcefield是用的compass, thermostat is NHL. 结构优化之后就跑MD，在800K的温度下跑了超过100ps，但是却没有看到任何分子的脱付。 不知道问题出在哪里。是我的体系不够大polymer分子不够多？还是其他的原因？ 谢谢 |
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2楼2013-11-15 13:49:23
pigrass
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月只蓝: 金币+1, 感谢指导！ 2013-11-15 15:49:48
月只蓝: 金币+1, 感谢指导！ 2013-11-15 15:49:48
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最好查下类似模拟的文献 关于系综在help里可以查到 NVE ensemble The constant-energy, constant-volume ensemble (NVE), also known as the microcanonical ensemble, is obtained by solving the standard Newton equation without any temperature and pressure control. Energy is conserved when this (adiabatic) ensemble is generated. However, because of rounding and truncation errors during the integration process, there is always a slight fluctuation, or drift in energy. During the data collection phase, if you are interested in exploring the constant-energy surface of the conformational space, or for other reasons do not want the perturbation introduced by temperature- and pressure-bath coupling, this is a useful ensemble. True constant-energy conditions (without temperature control) are not recommended for equilibration calculations because, without the energy flow facilitated by temperature control, the desired temperature cannot be achieved. Although the temperature is not controlled during true NVE dynamics, you might want to use NVE conditions during the equilibration phase of your simulation. For this purpose, some modules in Materials Studio allow you to hold the temperature within specified tolerances by periodic scaling of the velocities. The results can be used to calculate the thermodynamic response function (Ray, 1988). NVT ensemble The constant-temperature, constant-volume ensemble (NVT), also referred to as the canonical ensemble, is obtained by controlling the thermodynamic temperature. Some modules in Materials Studio allow direct temperature scaling, this should be used only during the initialization stage since it does not produce a true canonical ensemble (it is not truly isothermal). The typical temperature control scheme is based on the use of a chain of M Nosé-Hoover thermostats, in this case the observed quantity is: where Qi are the thermostat fictitious masses and ξi are the thermostat degrees of freedom. This ensemble is the appropriate choice when conformational searches of models are carried out in vacuum without periodic boundary conditions. (Without periodic boundary conditions, volume, pressure, and density are not defined and constant-pressure dynamics cannot be carried out). Even when periodic boundary conditions are used, if pressure is not a significant factor, the constant-temperature, constant-volume ensemble provides the advantage of less perturbation of the trajectory, due to the absence of coupling to a pressure bath. NPH ensemble The constant-pressure, constant-enthalpy ensemble (Andersen, 1980) is the analogue of constant-volume, constant-energy ensemble, where the size of the unit cell is allowed to vary. Enthalpy H, which is the sum of E and PV, is constant when the pressure is kept fixed without any temperature control. Although the temperature is not controlled during true (adiabatic) NPH dynamics, you might want to use these conditions during the equilibration phase of your simulation. For this purpose, some modules in Materials Studio allow you to hold the temperature within specified tolerances by periodic scaling of the velocities. Note: This method applies only to periodic systems. Pressure can be controlled by the Berendsen, Andersen, or Parrinello-Rahman method. However, only the size, and not the shape, of the unit cell can be changed with the Berendsen and Anderson methods. The constant of motion when the cell shape is fixed (Andersen) is: The Parrinello-Rahman method allows both the cell volume and its shape to change, so the constant of motion becomes: The natural response functions (specific heat at constant pressure, thermal expansion, adiabatic compressibility, and adiabatic compliance tensor) are obtained from the proper statistical fluctuation expressions of kinetic energy, volume, and strain (Ray, 1988). NPT ensemble The constant-temperature, constant-pressure ensemble (NPT) allows control over both the temperature and pressure. The unit cell vectors are allowed to change, and the pressure is adjusted by adjusting the volume (that is, the size and, in some programs, the shape of the unit cell). Note: This method applies only to periodic systems. Pressure can be controlled by the Berendsen, Andersen, or Parrinello-Rahman method. However, only the size, and not the shape, of the unit cell can be changed with the Berendsen and Anderson methods. Andersen-Hoover dynamics (Andersen, 1980) as corrected by Martyna et al. (1994) corresponds to the constant of motion: Stress can be controlled by the Parrinello-Rahman method, since it allows both the cell volume and its shape to change, the constant of motion is then: Temperature can be controlled by any method available (except, of course, the temperature scaling method, since it is not truly isothermal). NPT is the ensemble of choice when the correct pressure, volume, and densities are important in the simulation. This ensemble can also be used during equilibration to achieve the desired temperature and pressure before changing to the constant-volume or constant-energy ensemble when data collection starts. If the forcefield being used yields a high pressure at the experimental volume, it may be more realistic to simulate at the experimental pressure rather than the experimental volume. High simulated pressure is a sign that the system is unduly compressed, which restricts atomic motions, slowing down the dynamic relaxations. |
3楼2013-11-15 14:43:51