Dear David,
Thanks very much for your tips! This is a test case of restraining a
distance of 1.6 angstrom
between two water molecules (O--O). Yeah, I know that the restraints
have to fight against the
non-bonded interactions between the two waters.
For my real system, it is a Mg2+ in a TIP4Pew water box. And I want to
calculate the water exchange
rate using umbrella sampling for the Mg2+ model, following this paper:
http://pubs.acs.org/doi/pdf/10.1021/ct3000734
The distance for Mg2+ -- OW (H2O) is around 2.09 angstrom, maybe it is
impossible to restrain the distance to be 1.6 angstrom,
as you mentioned.
I didn't try to build a structure with a distance of 1.6 angstrom, so I
don't know about the force field energy.
Thanks!
All the best,
Qinghua
I
On 01/25/2017 08:06 PM, David Case wrote:
> On Wed, Jan 25, 2017, Qinghua Liao wrote:
>> I am doing umbrella sampling with amber16, the reaction coordinates are
>> the distances
>> between a metal ion and an oxygen of a water molecule. But I found that
>> the distance restraints
>> were failed for some windows. Here are my input files:
>>
>> &cntrl
>> imin = 0, nstlim = 25000, irest = 0, ntx = 1, dt = 0.002 ,
>> ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
>> ntp = 1, pres0 = 1.0, taup = 2.0,
>> ntb = 2, cut = 12.0 ,
>> ntc = 2, ntf = 1,
>> iwrap = 1, nmropt = 1 ,
>> ntwe = 5000, ntwx = 5000, ntpr = 5000, ntwr = 5000,
>> /
>> &wt
>> type='DUMPFREQ', istep1=50, /
>> &wt
>> type='END',
>> &end
>> DISANG=restraints.dat
>> DUMPAVE=distance.dat
>>
> Use LISTIN=POUT (say, right before the "DISANG=" line): this will print out
> details of the all of the restraints after they are read in, so you can check
> the input.
>
> Beyond that: do you have a bond between atom 345 and atom 425? If not, you
> are fighting the non-bonded repulsion between these two atoms, and no
> (reasonable) harmonic restraint will force you to a 1.6 Ang. distance.
>
> In fact, would probably get what you describe: distances that are around
> 1.9 or 2.0 Angstroms.
>
> So: if you manually create a structure with a 1.6 Ang. distance, what force
> field energy do you get?
>
> ....dac
>
>
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Received on Wed Jan 25 2017 - 12:00:02 PST
