On Fri, Jun 22, 2012, Elisa Frezza wrote:
>
> I am using AMBER 11 with PME and GPU.
> I simulated a pair of DNA in an octahedral box.
> The input file that I use is the following
>
> run: step 1 MD
> &cntrl
> imin = 0,
> irest = 0 ,
> ntx = 1,
> nstlim = 5000, dt = 0.002,
> ntc = 2 , ntf = 2,
> ntt = 3, gamma_ln = 2.0,
> ntp=1, taup=1,
> pres0=1,
> tempi = 100.0, temp0 =100.0,
> ntb = 2 ,
> ntpr = 250 , ntwx = 250, ntwr = 500 ,
> cut = 9,
> ioutfm = 1
> ntr=1
> /
> &end
> Keep DNA fixed with weak restraints
> 1000.0
> RES 1 136
> END
> END
> | ERROR: max pairlist cutoff must be less than unit cell max sphere
> radius!
Try equilibrating at constant voume to the final temperature you want, then
turning on constant pressure equilibration. Your solvent box is probably
quite small, and you would either need to make it bigger, or reduce the value
of "cut".
Aside: what you call "weak restraints" are actually way to strong. Consider
using values about 100 times smaller
...dac
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Received on Mon Jun 25 2012 - 05:00:03 PDT
