In case you get something along the lines of $ formchk input.chk output.fchk Read checkpoint file input.chk Write formatted file output.fchk Missing data for FChkPn. Error termination via Lnk1e at <DATE> Segmentation fault this means that your checkpoint file (*.chk) is damaged. Please make sure, that … … you have […]
computational chemistry
34 posts
Sometimes jobs need some local disk space for temporary data that should neither be part of the backup nor too slow to write huge amounts of data to. A common way to help users out is to define some scratch directory. Using PBS/torque, you can request access to this local […]
In case you get an error message similar to the following one directly after initialization, it’s pretty sure an issue with your checkfile. Most probably it does not exist – and this is Gaussian’s way of telling you so. In any case, you can use the strace command to see […]
Update Christopher Mayne wrote: ‘I’ve since not only corrected the portion of the code that throws the error, but added some lines to automatically detect linear elements and make the necessary changes to the Gaussian input file (i.e. “A” -> “L” and removing undefined dihedrals). These fixes are in our […]
If you do NPT simulations with namd2, you may get the following message: FATAL ERROR: Periodic cell has become too small for original patch grid! Unfortunately, namd2 does not support automatic restarts in this case. Here is a small wrapper script, that automates this process. Just prepare your namd.conf as […]
Gaussian sometimes gives error messages, that merely transport the information that something went terribly wrong. Of course, there is practically no hint on what Gaussian was trying to do at this point. On this page, I list the complete error messages and the corresponding solutions that worked for me in […]
In case you want to perform a relaxed scan of the potential energy surface for a given dihedral, you have to perform constrained (or at least restrained) optimizations. The namd way to do so is to define a collective variable (colvar in namd terminology) and then impose a harmonic potential […]
In case you get an error message of the form FATAL ERROR: Setting parameter binaryoutput from script failed! you should try moving the line specifying the parameter in question in your config file. In particular, the parameter has to preceed any command actually performing calculations. For example, this config file […]
As even the original publication on the TIP5P model does not include the exact definition of a kcal, the no-SI-unit-used-hell drives you crazy. The correct answer: the TIP5P model uses the thermochemical calorie which is exactly™ 4.184 J. Obviously, this conversion factor can be factored out easily as the total […]
In case you observe strange (long distance) bonds while animating a trajectory with VMD, this might be due to rearrangements of the molecule structure during the animation’s time frame. Sometimes, this behavior is not useful – especially, if you have lots of those conformation variations. In order to disable the […]