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Yu Du

  • Registered on: 10/24/2017
  • Last connection: 10/12/2019

Issues

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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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