CHARMM Development Project Forums User Discussion & Questions Molecular Dynamics Calculation of rmsd from NAMD coor file

The pdb files are necessarily read with an option (RESID or SEGI or CHAIN) because they are not native files. And if I don't add one of these options, charmm will write me that I am missing atoms.

Miscom.doc, paragraphe 27
judkil21 #38499 09/21/22 10:50 PM


It gives me an energy value that it has stored in memory ?

Is the question mark misused ? Because in miscom.doc, paragraph 27 it is written: "?" Energy value substitution

Thanks,

No. You should not use bomlev at all. It is to your benefit that the program stops when an error is encountered. And you also have to pay attention to warning messages.
You should not use commands at random.
You should only use commands that perform an action that you want, and that you understand. It is of course OK to experiment and see what happens - this is encouraged! How else could your learn?
You should consult with your supervisor - the forums are most definitely not a substitute for the guidance of a supervisor.

Also please understand that the testcases are mainly just that - they test the code. So while they may show what can be done and how, they do not really tell you what is the best way to achieve your objective.

No. You should not use bomlev at all. Why do you think you need this? It is to your benefit that the program stops when an error is encountered. And you also have to pay attention to warning messages.
You should not use commands at random.
You should only use commands that perform an action that you want, and that you understand. It is of course OK to experiment and see what happens - this is encouraged! How else could your learn?
You should consult with your supervisor - the forums are most definitely not a substitute for the guidance of a supervisor.

Also please understand that the testcases are mainly just that - they test the code. So while they may show what can be done and how, they do not really tell you what is the best way to achieve your objective.

Oh, "limit exceeded" means that the program is trying to use a memory location which it does not have access to - in plain language, chaos and disaster!

Ok thanks for your advice

No, what you do is correct, the documentation is misleading; it should say that the value of in internal CHARMM variable is used.