try imaging the trajectory in ptraj. search the archives for discussion and
examples. look for "ptraj" and "image".
On Tue, Feb 10, 2009 at 5:35 AM, parul sharma <sharmaparul7373.gmail.com>wrote:
> Dear All,
>
> I did minimization of my peptide in tip3p box, and the pdb i am getting is
> 1000rst (see pdb attached), and then i proceeded with the molecular
> dynamics
> using the following input,
>
>
> constant volume molecular dynamics, 10.0 cut
> &cntrl
> imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10,
> tempi = 0.0, temp0 = 300.0,
> ntc=2, ntf=2,
> ntt = 3, gamma_ln = 1.0,
> scee= 1.2, nstlim =250000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
> &end
>
>
> however, when i view the pdb 1001rst (see pdb attached), obtained after
> molecular dynamics simulation, it shows distorted distribution of water
> molecules around the peptide. I would be very thankful if someone could
> help
> me out with this problem.
>
>
>
>
>
>
> --
> With Best Regards
>
> Parul Sharma
> PhD Student, Durban University of Technology,
> Durban,
> South Africa
>
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Received on Wed Feb 11 2009 - 01:16:59 PST
