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Yong Nam

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01/11/2011

10:56 PM GROMACS Bug #657 (Closed): Problem of the function 'do_constraint' in file pull.c
I have frequently used pull code of GROMACS with constraint and distance geometry.
Recently, I got a chance to take ...

11/05/2008

10:53 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
Created an attachment (id=321)
The last part of the force file
10:52 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
I am not sure if the variations of the output time-step can be explained by the
numerical error. Consider for example...

11/03/2008

05:04 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
The step size starts deviating around 8ps. (Since I set the single step size as 0.025ps, 8ps corresponds with 320 sim...

11/02/2008

08:28 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
I performed MD simulation for 200ns, not 100ns.
08:24 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
Created an attachment (id=317)
index file
08:24 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
Created an attachment (id=316)
itp file
08:21 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
Created an attachment (id=315)
gro file
08:20 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
Created an attachment (id=314)
top file
08:19 PM GROMACS Bug #246: Saving data with uneven step size in pullf.xvg file.
Created an attachment (id=313)
mdp file

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