Yes it is an imaging issue and is not a problem. Check the archives or the
cpptraj manual for details on how to fix it.
On Dec 15, 2015 1:59 AM, "Anasuya Dighe" <anasuya.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am simulating a protein-ligand complex for a total of 100ns. The ligand
> in
> question is a peptide inhibitor, that is lodged in the catalytic cleft of
> the
> protein molecule. Upon completing the production run (spanning 100ns of
> data),
> I noticed some peculiar things happening in the trajectory.
> All of a sudden (at a random point in the simulation), the peptide
> inhibitor
> molecule was seen to be present at one end of the solvent box. It
> continued to
> be simulated there. The protein molecule was simulated at the other end of
> the
> box. Please mind the fact that this sudden behavior was not gradual in any
> sense ( i.e. the ligand was NOT exiting the catalytic cleft in a
> step-by-step
> fashion.)
> After a few (5-10) frames, the ligand went back to the cleft and this
> fluctuating behavior continued for around 10-12 ns, and after that the
> ligand
> was lodged in the cleft.The simulation otherwise completed after 100ns.
> Also
> please note that this behavior was NOT seen since the beginning of the
> simulation. In the beginning, the peptide was in the cleft. IT started all
> of a
> sudden at the 49th ns.
>
> I am quite puzzled at this picture. Is this an imaging issue?
> I am using the iwrap parameter as iwrap = 1
> The .in file for simulation is as follows :
>
> 1ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0, iwrap = 1,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2, ig = -1,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 500000, dt = 0.002,
> ntpr = 500, ntwx = 1000, ntwr = 100000
> /
>
> Please advice me about the steps to take in order to rectify this.
> Will something like this have an effect on the data analysis of the
> trajectory
> (using cpptraj)?
> Any special commands that i should use during cpptraj, in order to fix
> this?
>
> Thanks
> Anasuya Dighe
> C/o Prof. Saraswathi Vishveshwara,
> Lab No. 4, Molecular Biophysics Unit Annexe,
> Indian Institute of Science,
> Bangalore - 560012
>
>
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Received on Tue Dec 15 2015 - 03:30:04 PST
