[gmx-users] Extend Umbrella Windows

Justin A. Lemkul jalemkul at vt.edu
Mon May 28 15:33:18 CEST 2012

On 5/28/12 5:45 AM, Steven Neumann wrote:
> Dear Justin and Gmx users,
> I want to extend my simulation in each window of 20 ns. For this purpose I
> should use (example - window 0):
> tpbconv -s umbrella0.tpr -extend 20000 -o umbrella0extend.tpr
> mdrun -s umbrella0extend.tpr -cpi umbrella0.cpt -deffnm umbrella0 -pf pullf0.xvg -px pullx0.xvg
> My questions:
> 1. Do I have to use -deffnm , -px, -pf or without this my files will be updated
> to the one produced before?

Assuming you are using the latest version of Gromacs, -append is default and as 
such the file names recorded in the .cpt file should be used.

> 2. Will the umbrella0extend.tpr shall be used for a g_wham or my previous
> umbrella0.tpr combined with umbrella0extend.tpr? How to combine them?

It may or may not matter which you use, since the information pertaining to the 
umbrella sampling itself is not different.  You can't combine .tpr files; 
there's no need to.  In your case, umbrella0.tpr contains information for the 
first time interval and umbrella0extend.tpr contains that same interval plus 20 ns.



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


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