Hi,
Can you send me off-list a topology and coordinate file illustrating
the problem? Thanks.
-Dan
On Sun, Jul 30, 2017 at 11:33 PM, Meng Wu <wumeng.shanghaitech.edu.cn> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jul 31 2017 - 06:00:06 PDT
