On Fri, 2014-04-04 at 12:47 +0200, Urszula Uciechowska wrote:
>
> Dear amber users,
>
> I am running MD for DNA+protein, in one of my input I would like to use
> igb=1, below is my input file. Could someone have a look at it at check if
> its correct? I have never done Md for igb=1 before.
>
> production
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 0, ntp = 0,
> taup = 2.0, igb = 1,
> cut = 12, ntr = 0,
This cutoff is way too short for GB simulations in my opinion. I
usually set cutoffs to ~1000 A ( equivalent to no cutoff) for GB
simulations.
> ntc = 2, ntf = 2,
> tempi = 298.15, temp0 = 298.15,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 200, ntwx = 200, ntwr = 200
YOu are probably printing out energies, restarts, and coordinates too
frequently (especially if you are using a GPU).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 04 2014 - 04:30:08 PDT
