On Wed, Nov 25, 2015 at 8:24 AM, jinfeng liu <jinfengliu1119.gmail.com> wrote:
> ntc=1,ntf=1,iwrap=1,
TIP3P is a rigid water model and requires the use of SHAKE. So you
need at least ntc=2 here.
-Dan
> ntp=1,taup=2.0,
> cut=12.0, ntb=2, igb=0,
> ntpr=1, ntwx=1, ntwr=1,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
> Actually, I was not performing the strict MD simulation. I performed a
> QM/MM-like MD simulation, where the water molecules in the QM zone could
> exchange with those in the MM zone, by using the combination of Amber and
> my own program.
>
> 2015-11-25 23:02 GMT+08:00 David A Case <david.case.rutgers.edu>:
>
>> On Wed, Nov 25, 2015, jinfeng liu wrote:
>> >
>> > Recently, I performed molecular dynamics of the liquid water in TIP3P
>> > model. After the system was heated to 300K and equilibrated in 300 ps, I
>> > run the producution simulation. The temperature was controlled using the
>> > Langevin dynamics (ntt=3, gamma_ln=2.0) durig the production simulation.
>> > However, the equilibrium temperature (305K) was slightly higher than the
>> > target temperature which was 300K.
>>
>> Something is wrong here. Can you post your mdin file? I fear that some
>> unexpected combination of input parameters is leading to this result.
>>
>> ....dac
>>
>>
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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Received on Wed Nov 25 2015 - 09:00:03 PST
