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Marvin Bernhardt

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10/01/2019

11:13 AM GROMACS Bug #2950: wrong temperature reported at end of sim with uneven number of steps
Thanks for taking care of this.

09/30/2019

03:59 PM GROMACS Bug #2950: wrong temperature reported at end of sim with uneven number of steps
Any tip on how to provoke the wrong temperature without running all 333333 steps?
I tried with 3333 steps, but don't...

08/26/2019

01:49 PM GROMACS Bug #3067 (Closed): constraints = all-angles does not convert angles to constraints
I try to simulate united-atom propane gas (no LJ) with fixed C-C-C angle. For this I simply try to set constraints = ...

05/13/2019

04:26 PM GROMACS Bug #2942: Pressure not converging with semiisotropic scaling and wall restraints
Thanks!
03:13 PM GROMACS Bug #2950 (Closed): wrong temperature reported at end of sim with uneven number of steps
For one of my simulations i get a temperature of 3000 K reported for the last bit of 333333 steps, where it was equil...

05/10/2019

06:16 PM GROMACS Bug #2942: Pressure not converging with semiisotropic scaling and wall restraints
That is a good argument. I took a second look at the manual and the code and I think my intuition was wrong. Thanks f...
02:29 PM GROMACS Bug #2942: Pressure not converging with semiisotropic scaling and wall restraints
Thanks for pointing out, where in the code the virial for the restraints are computed.
Since I have refcoord_scali...

05/09/2019

11:52 AM GROMACS Bug #2942: Pressure not converging with semiisotropic scaling and wall restraints
Another system one might consider is a cuboid of fluid surrounded by vacuum as explained in the restraints help[1].
...
11:20 AM GROMACS Bug #2942: Pressure not converging with semiisotropic scaling and wall restraints
You are right, this is a complex issue and in the end is a question of definition.
The reason, why I was puzzled i...

05/08/2019

03:44 PM GROMACS Bug #2942: Pressure not converging with semiisotropic scaling and wall restraints
Thanks for the answer. I did not have the idea to look at pressure components yet. Neither to set the target pressure...

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