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jose flores-canales

  • Registered on: 05/09/2019
  • Last connection: 09/21/2019

Issues

Activity

09/21/2019

02:21 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
Amazing news! Thanks a lot Berk and your team for this detective work. I will test the patched GMX2018 ASAP.

09/18/2019

03:06 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
I haven't found irregularities on the head group planes and an obvious cavity is difficult to find. This membrane is ...

09/05/2019

02:47 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
Berk Hess wrote:
> A question about other MD packages. Do other packages have a coupling option equivalent to "semi-...

08/30/2019

11:01 AM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
I have been thinking about it, but I think I will settle down with initial semiisotropic NPT equilibration (~50 ns) f...

08/29/2019

05:23 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
It is my own system, a GPCR on POPC lipids bilayer and TIP3P. I have struggled with this for some months. For the tim...
03:11 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
I don't have enough statistical sampling, but the box is stable with pmemd.cuda engine. Following Berk's suggestion, ...

08/28/2019

04:01 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
I think this is expected. Once I forgot to choose isotropic NPT in a protein-solvent system. Instead the simulation r...

08/23/2019

04:52 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
I am running MD with AMBER18/pmemd.cuda using a restarting file before my system underwent transformation.

08/21/2019

03:25 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
I attach my mdp parameters file. It is basically the same from Charm-gui, except that I am using Langevin thermostat....

08/14/2019

01:04 PM GROMACS Bug #2867: abnormal box fluctuations on GPUs still there
Michael Shirts has mentioned that a Monte-Carlo barostat is on the works in his lab. It will be great to see this and...

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