Hi Daniel,
Many thanks for your email.
I fully agree that "everything is periodic"
I well familiar with the scientific background of the periodic cell approximation
accepted in MD simulations of a real macroscopic system of water solvated protein molecules.
In fact I wrote in my email about a drift of one protein molecule relative the frame
of truncated octahedron periodic cell observed in the 3D image generated by cpptraj,
when I used the following script despite the containing autoimage parameter:
parm ../mc.prmtop
trajin md_prod17.rst
autoimage origin
trajout md_prod17_100ns.pdb pdb
run
quit
All the best,
Michael
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Wednesday, September 20, 2017 3:35:22 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Protein drifts out of the periodic cell
Hi,
On Wed, Sep 20, 2017 at 5:21 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> During MD production simulations the protein
> has been drifting to the border of the periodic cell
> with a tendency of going out of it.
With periodic boundary conditions, nothing is ever really out of the
cell because everything is periodic. To make things look nicer you can
post-process the trajectory with the 'autoimage' command from cpptraj,
which will center and re-image your trajectory so that your solute
appears to be in the center of the unit cell. See the manual for full
details.
-Dan
>
> I need your advice what a key parameter should I add
> to the MD simulating script in order to prevent
> the protein drifting out of the periodic cell?
>
> See MD simulation details below.
>
> Thank you,
> Michael
>
> The protein was solvated in octahedral
> periodic cell applying TLEP procedure:
>
> solvateoct mc TIP3PBOX 15
>
> I used the following command lines to run production MD simulations:
>
> setenv CUDA_VISIBLE_DEVICES '2,3'
> nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i md_prod1.in -o md_prod6.out -p ../*.prmtop -c md_prod5.rst -x md_prod6.mdcrd -r md_prod6.rst -ref md_prod5.rst &
>
> The production MD simulation script, md_run.in, is:
>
> mc: 100 ns production phase MD
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 1.0,
> cut = 10.0, iwrap = 1,
> ntc = 2, ntf = 2,
> tempi = 310.0, temp0 = 310.0,
> ntt = 3, gamma_ln = 0.5,
> nstlim = 50000000, dt = 0.002, barostat=2,
> ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
> /
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 20 2017 - 09:00:02 PDT
