Yes, I have tried. My ambertools version now is 17.05, but the problem still exists.
My command to re-image the trajectory is:
parm DDM_130_1.prmtop
trajin 07_Prod_DDM_[X]1.nc
trajin 07_Prod_DDM_[X]2.nc
reference DDM_130_1.inpcrd
center reference ':1-130&!.H'
autoimage
trajout DDM_1_2_[X]pbc.nc netcdf
and to calculate the Rg is:
parm DDM_130_1.prmtop
trajin DDM_1_2_[X]pbc.nc
radgyr :1-130&!(.H=) out DDM_200ns_1_rog.dat mass nomax
I am still not sure enough the PBC problem will affect my calculation of the Rg of the micelle including all molecules or not. Any suggestions would be greatly appreciated.
All the best,
Meng Wu
------------------------------
Date: Fri, 28 Jul 2017 00:40:44 -0400
From: Hai Nguyen <nhai.qn.gmail.com>
Subject: Re: [AMBER] PBC problem with autoimage&image
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAFNMPM8AX6KPeSv1futOYVzcufLB+0x84um3m+tU1p_cBqXbNQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
have you tried cpptraj in ambertools 17 yet?
Hai
On Fri, Jul 28, 2017 at 12:37 AM, Meng Wu <wumeng.shanghaitech.edu.cn>
wrote:
> Dear All,
>
> I have simulated a micelle in the water with Amber16, but when I tried
> to re-image the trajectory usimg autoimage (I also tried image center
> familiar), I found it's hard to get all the micelle molecules in a box, I
> mean there were always a few molecules outside the box. My micelle is in a
> sphere and I want to see how its radius changes over time, so I would like
> to analysis its radius of gyration using 'radgyr', but the problem is I'm
> not sure if the above-mentioned PBC problem will affect my calculation of
> the Rg of the micelle including all molecules. If yes, how could I solve
> the PBC problem?
>
> Any suggestions would be greatly appreciated.
> Thank you in advance!
>
> All the best,
> Wu Meng
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jul 30 2017 - 21:00:03 PDT
