Frequently Asked Questions

Why has the generation of the potential failed?

In most cases this could be related to an unappropriate selected charge. Check that the charge that you provided fits the defined chemical system.

How can I set up my experiment?

NEXTMOL offers a list of available molecules to build your system. If your system of interest cannot be built with these molecules, polymers can be created using the NEXTMOL Builder, while small and medium-sized molecules can be created in the ‘Molecules’ section in NEXTMOL Modeling. We recommend to use one of the preassembled workflows that are available in the platform and to modify it to meet the requirements of the system. If you are unsure about the procedure to build the system, contact support@nextmol.com and we will assist you.

How can I check on the progress of a calculation?

In the Dashboard, the left menu will display the ‘Jobs’ section. There you will find the list of all the jobs that have been run in your account. Select any in-progress job and click on ‘Execution’. A detailed description of the process will be shown, indicating the percentage of progress of the on-going node.

Can I restart one calculation?

It is possible to restart a calculation if the job has reached the execution time limit. In that case, go to the ‘Execution’ tab in the job and click on ‘Execute job’. The calculation will restart following the progress of the previous job.

Can I reuse the nodes of one calculation in another one?

Yes, it is possible to reuse the parts of a job that are identical to the current one. For that purpose, after clicking on ‘Create job’, go to the ‘Reuse completed nodes from job’ and select the desired job. Note that the nodes that are not identical will be calculated once again.

How can I compare the results of two different jobs?

After performing the corresponding analysis, go to the left panel menu and click on ‘Data Analytics’. There you will be able to visualize the analysis that you select, facilitating the comparison.

The 'Fill Cell' node has failed, how can I fix it?

The 'Fill Cell' node allows to define the number of replicas of different molecules in a system, but it is the responsability of the user to ensure that the system fits the size of the box. In most cases, failure of this node can be solved either by increasing the size of the cell or by decreasing the number of molecules.

Why has my calculation stopped with an error status?

Many different factors can affect the success of a calculation. Here we include a summary of the most frequent ones:

  • If the calculation failed during a 'System operation' node, the problem is likely to be related to the geometry of the system. Check that there are no unrealistic settings in your system.

  • If the error happened during an energy minimization, in most cases this is a symptom of an excessively crowded initial structure. Decreasing the density of the system usually solves this issue.

  • If the calculation stopped during the execution of an NPT node, this could be related to a fast expansion/compression of the system. This issue could be solved by reducing the coupling constants in the advanced options of the thermostat and barostat. Note that for most cases a ratio of 1:5 in the coupling constants of the thermostat and the barostat respectively provides good performance.

If you have further questions, please contact support@nextmol.com .