Thank you.
I'll follow your advise.
Michael
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Wednesday, September 20, 2017 6:56:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Protein drifts out of the periodic cell
On Wed, Sep 20, 2017 at 11:35 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> 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:
I see - you didn't mention that you had used cpptraj in your original
message. The way 'autoimage' works is it uses an anchor molecule (or
region of a molecule) to center the system, then divides the rest of
the system into molecules that are "fixed" to the anchor and molecules
that can be imaged freely (like water). Cpptraj will by default choose
the first molecule as the anchor, but this is not always the best
choice. You may get better results by choosing a different molecule or
a specific region of a molecule (googling "cpptraj autoimage" will
give lots of examples). Without knowing more information (such as what
your system looks like) it's hard to provide more specific help.
-Dan
>
>
> 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
--
-------------------------
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 Wed Sep 20 2017 - 09:30:02 PDT
