Hi !
For solvated NVE simulations use something like this:
production npt 25ns
&cntrl
imin = 0, nmropt = 0,
iwrap=1, ntxo=2, ioutfm=1,
ntx = 5, irest = 1,
ntpr = 5000, ntwr = 5000,
ntwx = 5000, ntwe = 5000,
cut = 15.0, nscm=0,
ntt = 0, ig = -1,
TEMP0 = 300.0, TEMPI = 300.0,
nstlim = 25000000, ntc = 2, ntf = 2, dt = 0.001,
ntb = 1, ntp = 0, tol = 0.0000001,
/
&ewald
dsum_tol=0.0000001,
/
END
END
Greeting,
Hector.
> Dear professors:
>
> Recently, I simulated polypeptides in aqueous solution in a 6.8 nm
> square system. First, following the tutorial presentations, I do min,
> heat, density, equil process.Then the system were calculated in NVT
> ensemble for 5 ns to reach balance, the script like this:
>
> Vol Ala30HX2Sol
>
> &cntrl
>
> imin=0,irest=1,ntx=5,
>
> nstlim=5000000,dt=0.001,
>
> ntc=2,ntf=2,
>
> cut=10.0, ntb=1,
>
> ntpr=20000, ntwx=20000,ntwr=-100000,
>
> ntt=3, gamma_ln=3.0, temp0=310.0,
>
> /
>
> Finally, a 5ns NVE simulation was conducted, the script follows:
>
> Ene Ala30HX2Sol
>
> &cntrl
>
> imin=0, irest=1, ntx=5,
>
> nstlim=5000000, dt=0.001,
>
> ntb=1, ntt=0,
>
> cut=10.0,
>
> ntc=2, ntf=2,
>
> ntpr=20000, ntwx=20000,ntwr=-100000,
>
> /
>
> But in the NVE simulation, I find that the total energy of the system is
> on the rise In the attached file, how this thing happened? should be the
> ETOT unchanged in NVE?
>
>
> --
> ---------------------------------------------------------------------
> ZhangMK
> +8623-63063582
> Chongqing Institute of Green and Intelligent Technology of Chinese
> Academy Sciences.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 14 2014 - 17:00:02 PDT
