Yu Du
Activity
05/31/2018
- 04:05 PM GROMACS Bug #2513: ref_t and temperature incorrect with coulomb-type = user
- I tried rlist=1.3 and again it's better, log file excerpt copied here:...
05/28/2018
- 04:32 PM GROMACS Bug #2513: ref_t and temperature incorrect with coulomb-type = user
- Berk Hess wrote:
> What temperature difference do you get?
>
> Since this uses the deprecated group scheme, it wo...
05/23/2018
- 09:14 AM GROMACS Bug #2513 (Feedback wanted): ref_t and temperature incorrect with coulomb-type = user
- Maybe, this is another bug of forcetables.cpp. Previous one is Bug #2286.
You can reproduce this bug with followin...
11/27/2017
- 02:36 AM GROMACS Bug #2301: Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'
- Justin Lemkul wrote:
> Yu Du wrote:
> > Justin Lemkul wrote:
> > > Can you please try my proposed solution? Irresp... - 01:42 AM GROMACS Bug #2301: Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'
- Justin Lemkul wrote:
> Can you please try my proposed solution? Irrespective of the number of chains, the only way t...
11/26/2017
- 03:22 PM GROMACS Bug #2301: Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'
- Justin Lemkul wrote:
> Indeed, the NH chain terms are not there. But this is the default behavior as these quantitie... - 11:17 AM GROMACS Bug #2301: Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'
- Berk Hess wrote:
> The .edr file is not part of the rar file. I need that to see what is wrong.
Sorry for making ... - 02:58 AM GROMACS Bug #2301: Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'
- RAR file is attached. The program procedure is in the txt file.
11/24/2017
- 03:43 AM GROMACS Bug #2301 (Closed): Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'
- I want to choose the last N frames from nvt-normal2.trr as starting coordinates and velocities.
@gmx grompp -quiet...
11/02/2017
- 04:34 AM GROMACS Bug #2286 (Closed): Coulomb energies and forces incorrect with coulomb-type = pme-user
- Under group cutoff-scheme, simulation temperature only accords with the ref_t in nh-chain-length=1 in nose-hoover the...
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