> On Apr 19, 2015, at 9:27 PM, Shukla, Saurabh <sshukla4.illinois.edu> wrote:
>
> Dear Amber Community,
> I am using a protein which is a homodimer. Since I am new to simulation, in the initial simulations, I had not given the nscm commend in the input file. Therefore, one of the chain of the dimer has gone outside the periodic box in half of the frames in the trajectory. In such scenario, mirror image of the chain comes in the simulation box which is away from its another bound chain. It gives a impression that there are 2 molecules simulating far apart in different corners of the simulation box.
>
> When I performed RMSD analysis of the trajectory, It is giving weird graphs where RMSD shoots to very high value when one of the chain of dimer goes out of the box. Please suggest how can I solve this problem and align the protein properly for the simulation.
Note that proper “alignment” of the system is almost always unnecessary for simulations. It is often important for analysis, but the simulation spans all periodic images of a unit cell so imaging artifacts such as these have no impact on simulations.
If you are analyzing your simulations with cpptraj, make sure you use the command “autoimage” in the beginning of your cpptraj script to make sure that the system is properly centered in the unit cell and imaged properly.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 20 2015 - 06:00:08 PDT
