Thomas Cheatham writes:
>
>> "Todd J. Minehardt" writes:
>> >hi folks.....set up a simulation just as i always do, nothing fancy.....when i try to minimize it,
>> >i get the following message:
>> >
>> >the first lines in min.out are
>> >
>> > NSTEP ENERGY RMS GMAX NAME NUMBER
>> > 1 nan nan 3.3290E+10 CZ 11209
>> >
>> > VDWAALS = ************* EEL = nan HBOND = 0.0000
>>
>> You have atom overlaps (vdw and EEL are huge, bonded terms are reasonable).
I should also mention that one of the overlaps is the atom CZ (#11209) with
a very large gradient. It might help to look at that specific atom and its
neighbors-- are they close to the box edge? Or in the middle? You'd be amazed
how some crystal structures have overlapping atoms!
Dave
Received on Fri Jul 13 2001 - 15:07:41 PDT
