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Yang Ye

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11/19/2007

07:56 PM GROMACS Bug #177: position and velocity set to nan
Thanks. I am aware for the effects of the fix.

11/16/2007

11:23 PM GROMACS Bug #177: position and velocity set to nan
Created an attachment (id=257)
test case
test file including force field and run files.
type "grompp" and "mdrun" t...
11:18 PM GROMACS Bug #177 (Closed): position and velocity set to nan
it is an customized FF with section
[ dihedraltypes ]
; i l func q0 cq
;added by Dongsheng
O...

09/12/2007

09:25 AM GROMACS Bug #156: pdb2gmx generate wrong topology with uncorrect named H in pdb
i see. Apparently, I don't have any problem with such behavior. The user shall always do the checking.

09/11/2007

08:00 PM GROMACS Bug #156: pdb2gmx generate wrong topology with uncorrect named H in pdb
I have used
pdb2gmx -f npro.pdb
adding -ter results the same.
Only removing NPRO from aminoacid.dat can trigger a...

09/10/2007

02:50 PM GROMACS Bug #156: pdb2gmx generate wrong topology with uncorrect named H in pdb
I think this is not force-field specific but about how pdb2gmx deals with h-atoms. Of course, the root cause is the i...

06/30/2007

03:53 PM GROMACS Bug #156: pdb2gmx generate wrong topology with uncorrect named H in pdb
Created an attachment (id=216)
problematic PDB file
03:53 PM GROMACS Bug #156 (Closed): pdb2gmx generate wrong topology with uncorrect named H in pdb
Use attachd pdb which contains NPRO to generate topology with AMBER 99 port from Stanford. The result is additional H...

01/31/2007

11:17 PM GROMACS Bug #128: subtitle still shown with -noxvgr option
Created an attachment (id=105)
fixed source files

01/29/2007

03:52 AM GROMACS Bug #128 (Closed): subtitle still shown with -noxvgr option
Some analysis tools still print @subtitle with -noxvgr option set. I have made
the fix here.
http://www.ntu.edu.sg/ho...

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