| 5:49:17 AM PDT - Mon, Jun 22nd 2015 |
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I am running a molecular dynamics simulation on a small molecule for which reported force field does not include bond stretching parameters. When I use just these reported Lenard-Johns parameters, bonds break and I do not have a true molecule. When I add excess parameters for bond stretching, Although is not a correct manner, I get a positive value for total energy that resembles my system is not stable. Also I tried to define these bond lengths as z-matrixes in segment file according to some segment files in the test folder, but I got " Fortran runtime error: End of file". Any help is appreciated.
Best Regards
Saeed
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