Thank David and Jason for your valuable responses. It helps me to
understand a lot about choosing parameters.
One more thing I have down is that if in a crystal structure, 10
continuous residues are missed entirely (both backbone and sidechain),
but this part is not in the interaction region. Should I use some
program to build the missing residues, such as MODELLER? Or can I use
the crystal structure with missing part?
Thanks in advance.
Regards,
Binh
Quoting David A Case <case.biomaps.rutgers.edu>:
> On Thu, Apr 04, 2013, nguyentb.bii.a-star.edu.sg wrote:
>>
>> I'm an new user in AMBER, and hence, I have a lot of downs when
>> choosing parameter for particular ensemble.
>
> We chose default parameters with care, so (as a new user) you should be
> careful in modifying them.
>
>> I want to run NVE simulation, the paramaters I set are following:
>>
>> dt=0.002, # time step (ps)
>
> This is OK, but energy conservation will be considerable better with the
> default value of 0.001.
>
>> cut=14.0, # specific the nonbonded cutoff, in Angstroms
>
> Ouch...this does no good with periodic boundary conditions; consider
> using the
> default value (or perhaps something like 9 or 10.)
>
>> ntb=1, # periodic boundary, constant volume
>> taup = 0.1, # pressure relaxation time (in ps)
>
> This is ignored, since you are not using a barostat.
>
>> temp0=300.0, # reference temperature
>
> This is also ignored, since you are not using a thermostat.
>
>> /
>>
>>
>> Would you mind telling me whether the parameter is suitable for NVE
>> ensemble? If I choose taup = 0.1, does my simulation change to NPE or
>> NPV?
>
> No: ntp and ntb determine whether you are doing a constant pressure
> simulation.
>
>> Do I need to set the ntp=0 and tempi=300.0?
>
> No: ntp=0 is the default, and tempi is ignored when irest=1.
>
>> How about iwrap = 1,
>> tol=0.000001 (SHAKE) and dsum_tol to 10**-6 ?
>
> Setting these will give slightly better energy conservation, and
> hence I would
> recommend it.
>
> Your questions are good ones, than many people probably have. We developers
> should re-look at the descriptions of these parameters in the manual to make
> answers like this more clear.
>
> ...dac
>
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Received on Thu Apr 04 2013 - 06:00:04 PDT
