[gmx-users] why the values is not equal!

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 3 14:14:16 CEST 2005

chiloo Laohpongspaisan wrote:
> Dear all,
> I've run MD 500,000 steps (1000 ps). After the job ceased, i took the 
> last configuration of structure (file:  structure.gro), and ran MD 
> more with the same input file. But i don't understand that why the 
> properties of the last step of first MD is not equal to the zeroth step 
> of the second MD. Below is the MD results of 1st MD and 2nd MD, 
> respectively. And my MD paramerter file is as follow.

The .gro file only has the coordinates and velocities to a lower 
precision than is used internally, and doesn't have information about 
any temperature or pressure coupling. Thus your restarts are actually in 
a different state to the one that you finished the previous run in. To 
make a restart work like you want it to, you need to give either grompp 
or tpbconv the previous trajectory (.trr) file and energy file (.edr) 
also as inputs. See the manpages and manual.

Mark Abraham

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