OneAngstrom

Hello,

Thanks for your interest in SAMSON! If you’re on Windows, you will need to install the latest runtime from Microsoft. They are available here: https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads.

You should install vc_redist.x64.exe available from that page.

Best regards,

Stephane

@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!

Hello, could you please try to add it in the Additional parameters section of the Simulate tab? (Under "Saving interval", you should see the "All..." push button.

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?