On 4/24/2013 7:51 PM, tec3.utah.edu wrote:
>> 2. the first step of the MD gives ***** even if I start the temp at 0 and
>> raise it to 3K with dt=0.00001, and shake off and
>>
>> I will keep minimizing...
> What I often suggest is to try minimizing first with electrostatics turned
> off; this often fixes clashes (although this will not recover from ring
> fusions, e.g. when a chain and a ring overlap, miminimization can put the
> chain the in middle of a ring).
>
> min_noelec.in (w/out water):
>
> production
> &cntrl
> imin = 1, maxcyc = 25000, ncyc = 25000,
> ntb = 0,
> cut = 9.0,
> nmropt = 1, ntpr = 500,
> &end
> &wt
> type = 'ELEC', value1 = 0.0,
> &end
> &wt
> type = 'END',
> &end
> &rst
> iat = 0,
> &end
At the other extreme, the nonbonded-free force field of xleap will never
get stuck bond-thru-ring.
Bill
>
> --tec3
>
>
>
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Received on Wed Apr 24 2013 - 22:00:02 PDT
