Thank you for your answer.
I have another question, If I setup a simulation with tempi=0.0 and
temp0=298.0 and a total running time of 1 ns, how much time will take to for
temparature equilibration???
Anthony
On Friday 26 August 2005 9:16 am, Carlos Simmerling wrote:
> the initial structures can be the same or not, both have
> been used in published studies. The conformations can be random,
> from equilibrated runs, etc. They can be equilibrated in advance
> or they you can discard part of the REMD results as the equilibration
> period. Temperature spacing depends on system size and should be
> exponential, articles have been published on optimal replica
> spacing (do a google search for replica exchange optimal spacing).
>
> Overall, REMD provides many more options than normal MD and
> you'll need to read the literature to see what others have done.
> It's not a method to use until you are very comfortable with regular
> MD and especially with analyzing simulation convergence. REMD is not
> magic and you need to be much more careful with convergence than
> you need to be with normal MD (since many REMD simulations can
> appear to be converged long before they really are).
>
>
>
> quoted message:
> I am trying to run a replica exchange simulation. I have some doubts in how
> to setup the system. First, the initial structure for each replica is the
> same or different conformations??? If different conformetions are needed,
> how to obtain those conformations. Second, the initial structure for the
> replicas need to be at the temp0 specified in the mdin? or all replicas
> start for the same temperature (tempi=0.0 temp0=temp) of the replica?.
> Third and last, How to select the temperatures for the replicas?? any
> method???.
>
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Received on Fri Aug 26 2005 - 17:53:00 PDT
