On Fri, Oct 16, 2015 at 12:48 PM, Guqin Shi <shi.293.osu.edu> wrote:
> Hi Ross,
>
> thanks for the explanation. Let me re-interpret your email to make sure I
> understand what you've mentioned...
>
> 1. I am using ntt=1 which does not use random numbers. Does that mean
> whatever number I assign to ig, it doesn't matter at all? As long as I use
> ntt=1, each run will always be identical? (all the rest just read .rst file
> from last run)
>
Not quite. The temperature control does not depend on random numbers. So
given a fixed set of starting velocities and coordinates, the random number
generator will have no effect on dynamics.
However, if you set irest=0, ntx=1, and tempi to some number *greater* than
zero, then the velocities will be non-zero and set randomly from the
Maxwell-Boltzmann distribution (so it *will* depend on ig for these initial
velocities).
2. If I change to ntt=3, I also need to change tempi to non-0, for instance
> 1 K, in order to use ig=-1. Right?
>
No. tempi=0 is perfectly fine for ntt=3.
> 3. I don't have a specific reason to use ntt=1.
Then don't use ntt=1. There are known problems with the Berendsen
thermostat (it has been proven NOT to generate a correct canonical ensemble
in the general case). ntt=3 is a much better choice.
> If any, it might because I
> learned and obtained input files from senior labmates... My system is a
> very common, 100 residues, protein-small molecule complex. Currently in my
> lab, I am using Amber 14. The final goal for these multiple independent
> runs is to calculate binding energies. Can you give a common advice about
> the ntt I should use for equilibrium and run under NPT? I found some
> suggestion in tutorial (
> http://ambermd.org/tutorials/basic/tutorial1/section3.htm) but it's for
> NVT. Thank you very much!
>
The suggestions still apply to NpT and for the same reasons.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 16 2015 - 10:00:05 PDT
