Dmitriy Marin is a research engineer and co-founder at OneAngstrom (1-a.io). Until 2018, he was a PostDoc at the NANO-D research group at Inria that he joined in 2016. He received a PhD in Applied Mathematics and Computer Science in 2015 from Ufa State Aviation Technical University, Russia, while working with Prof. Nail A. Gumerov (University of Maryland) on the development of advanced methods and algorithms for GPU-accelerated systems in the application to molecular dynamics.
@carmine Thank you very much for your feedback!
We will add other box types in one of the next updates of the GROMACS Wizard.
Options provided in the Additional parameters have bigger priority then options specified in the GUI. It is true, it would be nice to highlight them in some way.
@carmine Great!
No, for now, GROMACS Wizard supports only the cubic box type, but we can add other box types in the future releases.
Could you, please, tell us what else you would like to see in the future releases of the GROMACS Wizard or in SAMSON in general?
For example, try decreasing the Integration time step to 0,001 ps.
@carmine said in GROMACS wizard - Letal Warning during NPT Equilibration step:
WARNING 1 [file PEP_1_prepared_minimized_nvt_2_boxed.top, line 48]:
The bond in molecule-type Protein_chain_A between atoms 61 OG1 and 62 HG1
has an estimated oscillational period of 9.0e-03 ps, which is less than 5
times the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
You may need to solve this GROMACS warning by either modifying the time-step or changing the constraints mdp options.
GROMACS stops due to GROMACS warnings. Did you add the -maxwarn option in the additional parameters of this step?
Note, different steps in the GROMACS Wizard (equilibration, simulation, etc) have their own parameters and you may need to specify additional parameters in each one of them.
@carmine
Great! Thank you for your feedback!
Apparently, there are more warnings or the -maxwarn option did not take effect at all. Does the error log show you the same warning or more? If there is more, could you, please, post the log as you did before. It will be very helpful for us. Meanwhile, in the Additional parameters, you can try increasing the maximum number of warnings, e.g.:
-maxwarn 10
Thank you!
Dear @Tadija
This just means that SAMSON was not able to get the name of the GPU but it should have detected it properly. Does SAMSON work properly for you or you experience some problems with graphics?
Yes, this is a default Element, meaning every user has it by default when he/she registers. Default Elements (e.g. basic impoters, exporters, state updaters) are not shown in the list of SAMSON Elements, but they are shown on the My SAMSON page (you need to be logged in to see it) from where they you can remove them from your SAMSON installation or add them again later.
Log in on SAMSON Connect, follow the State Updater Pack Element link and click Add.
Thank you for submitting the log! We will check it.
Do you have the State Updater Pack Element added from SAMSON Connect?
If you don't find these lines with StateUpdaterPack in the log, it means that you do not have this Element added and installed.