[gmx-users] Extend Umbrella Windows

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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