Subject: Re: your mail

From: Dan Severance <[email-masked]>
Date: Thu, 6 Aug 92 20:38:01 EDT

> 
>    We have been trying to run a PMF calcuation for a system of two 
> solutes in a box of TIP3P water using BOSS version 2.7.  The first 
> step of the simulation appears to work fine; however, all attempts
> to continue the simulation using the option ISTART=3 have resulted
> in values of 'Infinity' being written to the UP file. The ISTART=3
> option is the recommended choice for beginning the next step in a
> free energy perturbation calculation. Has anyone encountered this
> problem as well?  Any suggestions for a fix would be  greatly
> appreciated.  
> 
    Hi Bob,
       Try running the 311 simulation for 50,000 configs or so, and
  then instead of using 001 on the next step, use 011 to restart
  averaging (this will recreate the upfile).  By that point the initial
  bad interactions which led to the infinities will have been resolved
  and furthur writes to the upfile will be fine.  You can then do your
  normal 001 starts for the rest of the equilibration as usual...

       Dan Severance
       [email-masked]  ! No big .sigs !

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