AMBER Archive (2005)

Subject: Re: AMBER: REM error

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Tue Sep 13 2005 - 16:36:21 CDT

Thank you Carlos for all your help.

On Tuesday 13 September 2005 11:40 am, Carlos Simmerling wrote:
> I apologize for the manual not being more clear on this, we are working on
> a tutorial.
>
> Anthony Cruz wrote:
> >Ok.
> >I need to run a short equilibration MD first for all the replicas or just
> > one and the use this structure for all the replicas???
>
> run short MD (even a few steps is enough, just to get velocities) for
> any structure that you want to use for the initial structure. using the
> same inpcrd for all replicas is ok, but some people prefer to use
> different structures for each. that's up to you.
>
> >This little run at what
> >temperature will be if the lower temperature of the replica is 330k, (ex.
> >from 0 to 298 for 200ps)???
>
> it can be any T, the replicas will equilibrate during the simulation
> anyway. Just like normal MD, you will want to discard some initial
> period of REMD simulation as equilibration.
>
> >Then I need to set the tempi of all replicas equal
> >to the temperature of this littler run ???
>
> tempi won't be used since it is ignored if ntx=5 and irest=1. just set
> temp0 for the replicas.
> make sure that the input files are identical except for temp0 - we use a
> script to create the mdin files.
>
> >Anthony
> >
> >On Tuesday 13 September 2005 5:25 am, Carlos Simmerling wrote:
> >>Anthony Cruz wrote:
> >>>Thank you for your answer.
> >>>I find an error in the *.in files, :
> >>>I have this irest = 1, ntx = 5, and sander cand find the velocities
> >>> so I change it to irest = 0, ntx = 1, because I start all the
> >>> replicas with the same minimized structure.
> >>
> >>you need to use irest=1, ntx=5. Amber9 will have more
> >>extensive checking of REMD inputs. Just run a short equilibration MD
> >> first. The reason is that after each exchange the input is re-used and
> >>you need to have all of the data read from the restart file.
> >>carlos
>

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