I have investigated this issue with several test cases with both ptraj and
VMD (and checked the ptraj source code in action.c). Simply translating does
not take into account the gamma=120 angle of my unit cell, i.e. translation
does not reproduce the periodic images from my simulation. As a result, I am
not obtaining the correct interfaces in my filtered trajectory. Does anyone
know of a way to translate along unit cell dimensions that are not all
orthogonal to one another?
Sincerely,
Logan S. Ahlstrom
Ph.D. Candidate
Department of Chemistry and Biochemistry
University of Arizona
On Fri, Dec 10, 2010 at 6:21 PM, Logan Ahlstrom <logana.email.arizona.edu>wrote:
> I have run a simulation of six protein chains with non-orthogonal
> boundary conditions. Now I want to extract specific chains (i.e two of them
> at a time) from the trajectory in order to analyze interactions between
> them. Below is the script I am using in order to extract residues 1-66
> (chain 1) and 199-264 (chain 2) and then to translate chain 2 in the -Y
> direction. (Each chain is identical and is 66 residues long).
>
> trajin ../../../traj/PSQ_xtal/test.mdcrd 1 100 1
>
> box x 50.524 y 50.524 z 48.148 alpha 90.0 beta 90.0 gamma 120.0 fixx fixy
> fixz fixalpha fixbeta fixgamma
>
> strip :265-396
>
> strip :67-198
>
> center :1-132 mass origin
>
> translate :67-132 x 0 y -50.524 z 0
>
> trajout ../../../traj/PSQ_xtal/interface6/test.out.mdcrd nobox
>
> In the outputted two-chain trajectory, the second chain is translated in
> the correct direction but it does not show the same interface as in the
> original trajectory. Perhaps ptraj is treating gamma as 90.0 instead of
> 120.0 degrees, even though I am explicitly giving the program the box
> lengths and angles? I have tried input trajectories with/without periodic
> boundaries specified, as well. Any suggestions/input would be much
> appreciated.
>
> Sincerely,
>
> Logan S. Ahlstrom
> Ph.D. Candidate
> Department of Chemistry and Biochemistry
> University of Arizona
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Received on Sat Dec 11 2010 - 15:30:03 PST
