[gmx-users] DPOSRES not working

[Justin Lemkul]

On 9/7/17 5:28 AM, Sergio Manzetti wrote:
> Hi Johannes, yes, they are there in both cases:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_DNA_chain_E.itp"
> #endif
>

Do you have a position restraint energy term written in your .log file, 
and if so, what is its magnitude?  Does your DNA start at the middle of 
the box (GROMACS convention) or at the coordinate origin (like other 
software)?  If you watch the trajectory evolve, what happens?  Does the 
DNA move a lot or does it just bounce back and forth around its original 
position (suggesting your box is simply too small and any time an atom 
crosses a boundary, you get a jump)?

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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