[gmx-users] The equilibrium before REMD simulations

ÏéÇ« ¿× iconsdkxq at yahoo.com.cn
Mon Nov 14 15:12:04 CET 2011

Dear GMX users,
  I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help.
  With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of the papers about REMD, a short equilibrium with NPT or NVT was performed for each replica respectively before the final REMD run. But i think the initial structure of each replica for REMD run is thus different due to the respective equilibrium and may somewhat go against the concept of replicas which i suppose should have same initial structures while with different temperatures. So my question is whether we should or not perform the NVT or NPT equilibrium before REMD simulations BTW and why? BTW, i also want to know which ensemble should we use in REMD because some papers use NPT while others use NVT.  
 Thanks in advance!
 Best regards!
 Xiangqian Kong

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