Re: [AMBER] Change in boxlength during memebrane simulation

From: Sally Pias <sallypias.gmail.com> Date: Fri, 3 Aug 2018 15:55:35 -0600

--
Sally Pias
Associate Professor of Chemistry
Faculty Adjunct, Department of Biology
New Mexico Tech
sallypias.gmail.com
On Fri, Aug 3, 2018 at 8:59 AM, somdev pahari <somdevpahari1.gmail.com>
wrote:
> Hi All,
>
> I am new to membrane simulation and also in amber. I am using AMBER 12.0
> with AMBER 18 tools. The lipid is DMPC. For lipid I have used lipid17 and
> for water TIP3P model.
> <http://ambermd.org/tutorials/advanced/tutorial16/index.html>
>
> After minimization the box dimension was 70.617000  70.847000  72.789300.
> My simulation temperature is 300 K. Now after 70ns production run I notice
> that my box dimension is 50.049  81.694  61.070. I am unable to understand
> why this change happens. Is it normal behaviour for membrane or not or
> there has a any kind of mistake for set up the system? Below, I have shown
> the input file for production run, also I have attached the snapshot of the
> system after minimization and the corresponding system after it reaches
> 70ns production run and the graph for varying box dimension.
>
> Input File:
>
> Lipid npt_production 300K
>  &cntrl
>   imin=0,
>   ntx=5,
>   irest=1,
>   ntc=2,
>   ntf=2,
>   tol=0.0000001,
>   nstlim=500000,
>   ntt=3,
>   gamma_ln=1.0,
>   temp0=300.0,
>   ntpr=1000,
>   ntwr=1000,
>   ntwx=500,
>   dt=0.001,
>   ig=-1,
>   ntb=2,
>   ntp=2,
>   cut=10.0,
>   ioutfm=1,
>   ntxo=2,
>  /
>
>
> Kindly, help me
> Thanks in advance
>
> Somdev Pahari
> Research fellow
> National Institute of Technology, Rourkela
> Odisha
> India
>
> _______________________________________________
> 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