AMBER Archive (2009)

Subject: Re: [AMBER] long polymer chain and image command in ptraj

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Mon Apr 06 2009 - 03:15:00 CDT

Hi Iccy,

        The first thing I notice about your system is that you are simulating a
single polymer chain under PDC conditions. It is likely that the polymer is
interacting with its own image in the adjoined boxes. This is typically
something that you want to avoid. However, I am not sure if this cause the
imaging problem in ptraj. I suggest that you simulate several polymer chains
in one box under PBC conditions. (Note that this will introduce other
problems such as creating a random spacial and conformation distribution of
polymer chains if you want to simulate a melt.)

        If you are working on non-biological polymers and have made your own residue
prep files, double check the tacticity if it is present in your system. I
have had trouble getting leap to recognize the tacticity of our polymers

        Note that to reproduce many experimental observables in polymers require very
long time scales. This is typically very difficult to obtain using atomistic
simulations. Just getting the entanglement of a polymer system is very
difficult to do with atomistic simulations. An alternative is to do a
mesoscale simulation (sometimes called coarse grained) and then backmap the
beads to atoms. This is currently the cutting edge for polymer simulations
and is not standard.

        Hope that helps.

Cheers,
Karl

On Thursday 02 April 2009 21:11, iccy liu wrote:
> Hi, all,
>
> I met a challenge in my simulation and would like to hear experts' opinions
> about that. I started my simulation with an extended long polymer chain,
> solvated in water. my solvent box is a rectangle prism with one dimension
> much longer than other two. I set up periodic boundary condition in my
> simulation. During my simulation, I observed that one end of my polymer
> chain (sometimes two ends) moved out of the solvent box and the polymer
> also turned to fold together. I assum it is not a problem since the
> periodic boundary condition is actived. However I had a hard time to
> analysing my trajectroy. I tried to use image command and couldn't get a
> reasonable trajectory. Also because of my polymer folded, it is impossible
> to be fit in the original rectangle prism anymore. I wonder did anyone meet
> similar problems before? Any input will be highly appreciated.
>
> Thanks in advance,
>
> Iccy Liu
>
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-- 
------------------------------------ 
Karl N. Kirschner, Ph.D.
Fraunhofer-Institute for Algorithms
    and Scientific Computing - SCAI
Department of Simulation Engineering
Schloss Birlinghoven
53754 Sankt Augustin, Germany
Tel: +49 (0) 2241-14-2052
Fax: +49 (0) 2241-14-1328
------------------------------------ 

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