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 - 05:00:04 PDT
