On Wed, Apr 29, 2015 at 10:34 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Ross and Jaison,
>
> Thanks for the inputs. Regarding the value for 'ig', I am afraid to say
> that all my previous were done with default value for ig and simulations
> looked fine for me. Below is the details for MD input I used,
>
> &cntrl
> imin = 0, ntx = 5, irest = 1,
> ntpr = 100, ntwx = 1000, ntwe = 0, ntwprt=0,
> ntc = 2, ntf = 2,
> nstlim = 2500000, dt =0.002,iwrap=1,
> tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> ntb = 1, ntp = 0, taup = 2.0, pres0 =1.0,
> &end
>
>
> Do I need to worry about anything here? As you see, all my previous MD runs
> with protein-in-water were in NVT with ntt=1. What all modifications I
> should consider here, while doing microsecond of proteins in membrane?
>
ntt=1 is not a stochastic thermostat, so it is not subject to the
synchronization artifacts like Langevin dynamics is (ntt=3). However, the
Berendsen thermostat (ntt=1), also called the weak-coupling thermostat, is
known to not sample from the canonical ensemble. Langevin dynamics is a
much better choice (or, alternatively, ntt=2 -- the Andersen thermostat --
is also better, though I prefer Langevin).
So previous simulations are not "ruined" by using the default ig value, but
I would definitely suggest switching to a more rigorously correct
thermostat like ntt=3 (and in that case, you should also set ig=-1).
Note that some people use the Berendsen thermostat with a long coupling
constant (e.g., tautp=10) as a way of doing a sort of "corrected" NVE
simulation in which the velocity scaling is small enough to (hopefully)
minimally impact the simulation while at the same time correcting for
potential integration errors by bleeding the extra energy introduced by
that (or adding energy lost by that).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 29 2015 - 08:00:03 PDT
