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zhiyi wu

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11/29/2019

05:51 PM GROMACS Bug #3222 (Rejected): editconf change the name of carbon atoms
Say if I had a gro file which has a atom, which is named as C116.
If I use editconf to change it to pdb, the name C1...

11/21/2019

09:18 PM GROMACS Bug #3213 (New): Having a local residuetypes.dat for custom force field
I'm trying to port the amber lipid17 force field to Gromcas. However, since the amber lipid17 force field is a modula...

10/04/2019

05:14 PM GROMACS Bug #3122 (Rejected): Coul-SR reports numbers of unknown origin
Say I have a system composed of sodium and a chloride atom, which are separated by 1 nm. Under the non-periodic condi...

05/06/2019

07:51 PM GROMACS Bug #2941 (Closed): OpenCL fail in osx 10.13.6
I have compiled the gromacs 2019.2 in osx 10.13.6 with intel compiler and it gives
--------------------------------...

02/21/2019

04:15 PM GROMACS Bug #2865: OpenCL error with mdrun
I have compiled it with the gcc7 and it doesn't seem to work either.
10:56 AM GROMACS Bug #2865 (Closed): OpenCL error with mdrun
I have tried to compile the GROMACS 2019.1 and 2019.0 on OSX 10.13.6 with Radeon Pro 580 and intel compiler 2019.2.
...

12/12/2018

02:12 PM GROMACS Bug #2804 (Rejected): Cannot append trajectory after no append flag is used
Suppose I want to run a simulation and it failed half way after a checkpoint file has been written....

10/29/2018

11:23 AM GROMACS Bug #2717 (Closed): mdrun runs infinitely when checkpoint file is beyond the designated end point
Say I have a tpr file which I say in the mdp file for it to runs for 50 ns and I stopped the simulation at 31 ns.
If...

09/10/2018

11:16 PM GROMACS Bug #2639: Turning on soft-core coul changes the dhdl of a ligand which has partial charge of zero
I have checked and the pressure is indeed fixed and thus, I haven't compiled Gromacs wrongly.
11:12 PM GROMACS Bug #2639: Turning on soft-core coul changes the dhdl of a ligand which has partial charge of zero
Many thanks for fixing the bug. I have just compiled the new version and tested it. However, it seems that the proble...

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