You just observed the so-called "polarization catastrophe" ... this is
expected with the Applequist model, i.e. ipol=1 ... that's why we are
working with a new Amber polarizable force field based on the Thole
model.
You might prevent this if you are more careful in your heating process
... keep your fingers crossed ... Also install the latest Amber
release so it is easier for people to help you ...
Ray
On Thu, Jun 9, 2011 at 7:41 AM, Xioling Chuang <xioling_c.hotmail.com> wrote:
>
> Dear All,
>
> I am using amber9 to run MD of a small DNA duplex solvated in POL3 water model.
> First, I minimized WAT and counterions without any problem. Then, I run MD with restrained on DNA and I got an error message.
> Input file is
> =============
> 20ps MD with restrained on DNA
> &cntrl
> ntb = 2, ntp = 1,
> ntc = 2, ntf = 2,
> ntt = 3, cut = 9.0,
> ipol = 1,
> temp0 = 300.0, ntr = 1,
> gamma_ln = 1.0,
> nstlim = 20000, dt = 0.001,
> ntpr = 1, ntwx = 1000, ntwr = 1
> /
> Fix DNA
> 1000.0
> RES 1 8
> END
> END
> =============
>
> Here I tried to set ntpr=1 to see what happen. Please see attached file for the output.
> Any suggestion, please?
>
> Regards,
> Xioling
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 09 2011 - 09:00:02 PDT
