[gmx-users] About Umbrella spacing

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 30 16:56:07 CEST 2012

vidhya sankar wrote:
> Dear justin thank you for your reply.
>                                                          i Have got 
> Summary_distance.dat file as output 
> I need 0.02 nm Spacing For that I  Inspect Output .Dat file
> For some Distance i Have not obtained corresponding Coordinate files
> Example  as follows  After 148th frame I have not received  a Coordinate 
> file corresponding to  0.623145,
> i am getting only 0.6353225 which corresponds to 150th frame
> It means  spacing is not uniform Now what to do to get coordinate files 
> corresponding to equal spacing

I see two options. You can do the SMD simulation over again, saving 
configurations more often to capture an appropriate configuration, or you can 
use the coordinate file that is closest to the desired value, set the desired 
restraint distance explicitly (i.e. not simply using "pull_start = yes") and 
allow it to equilibrate for a while.


> frame        Coordinates 
> 139            0.5839833
> 148            0.6008763
> 150            0.6353225
> Thanks in Advance


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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