using explicit solvent mixed with continuum models can be difficult
and is still a research problem. you might want to try restraints, or else
remove these waters. in any case you can't let them float away, it will
cause
problems like what you've seen with the coordinates getting
too large.
mathew k varghese wrote:
>Dear simmerling,
>
>Thanks for your help.
>Yes, my system contains crystallographic waters which
>fly off into large distances as the temperature
>increases from 0K to 300K. Even when the temperature
>is fixed at 300K the water molecules fly off. How can
>I deal with this problem. Should I impose some
>restraints on the water molecules? If so how can I do
>that.
>thanking you,
>
>--- Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
>wrote:
>
>
>>you can't just delete data form the restart file,
>>then the
>>coordinates won't be given to the right atoms.
>>you need to solve the problem of the asterisks.
>>
>>it looks like some of your coordinates are larger
>>than
>>1000 angstroms, while others are much smaller.
>>did the MD that produced this file complete without
>>anything unusual, or any large energies?
>>is the system very large? is it more than 1
>>molecule? maybe
>>they have become separated very far in space.
>>you'll need to look at your system and find out what
>>is
>>happening to the structure to cause such large
>>coordinates.
>>
>>
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Received on Tue Apr 12 2005 - 14:53:00 PDT
