[gmx-users] Re:gmx-users Digest, Vol 113, Issue 54
aixintiankong
aixintiankong at 126.com
Fri Sep 13 15:25:35 CEST 2013
Dear prof.
after i calculating the secondary strucure of residues frome 20 to 60 using do_dssp . And then i use xpm2ps to show the picture with ps.m2p, but the residue order number of y-axis start form 1 not the 20. how can i change the order of residue? Thank you very much!
At 2013-09-12 18:00:06,gmx-users-request at gromacs.org wrote:
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>Today's Topics:
>
> 1. RE: average pressure of a system (Dwey Kauffman)
> 2. how to make a index file (aixintiankong)
> 3. RE: RE: average pressure of a system (Dallas Warren)
> 4. Re: RE: average pressure of a system (Tsjerk Wassenaar)
> 5. PhD vacancy on MD modelling at University of Groningen
> (Patrick Onck)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 11 Sep 2013 20:31:50 -0700 (PDT)
>From: Dwey Kauffman <mpi566 at gmail.com>
>Subject: [gmx-users] RE: average pressure of a system
>To: gmx-users at gromacs.org
>Message-ID: <1378956710192-5011137.post at n6.nabble.com>
>Content-Type: text/plain; charset=UTF-8
>
>Justin Lemkul wrote
>> On 9/11/13 12:12 AM, Dwey Kauffman wrote:
>>>> True, but thermostats allow temperatures to oscillate on the order of a
>>>> few
>>> K,
>>>> and that doesn't happen on the macroscopic level either. Hence the
>>>> small
>>>> disconnect between a system that has thousands of atoms and one that has
>>>> millions or trillions. Pressure fluctuations decrease on the order of
>>> sqrt(N),
>>>> so the system size itself is a determining factor for the pressure
>>> fluctuations.
>>>> As previous discussions have rightly concluded, pressure is a somewhat
>>>> ill-defined quantity in molecular systems like these.
>>>
>>> Dose it also imply that it is not a good idea to study the relationship
>>> between dimer (multimer) dissociation and macroscopic pressure in this
>>> case
>>> ? (due to the ill defined pressure).
>>>
>>
>> I would simply think it would be very hard to draw any meaningful
>> conclusions if
>> they depend on a microscopic quantity that varies so strongly.
>>
>>> It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8,
>>> 0.9, 1.0, 1.1, 1.2 ...., perform independent simulations, and then obtain
>>> outcomes of targeted quantities for comparison.
>>>
>>
>> As with the original issue, I would find it hard to believe that any of
>> the
>> differences observed in such a setup would be meaningful. Is 0.7 ± 100
>> actually
>> different from 1.2 ± 100?
>>
>>>>
>>>> You could try altering tau_p, but I doubt there is any value in doing
>>>> so.
>>>
>>> I would give it a try.
>>>
>>
>> This will really only change the relaxation time. Smaller values of tau_p
>> may
>> improve the average slightly, but may also (more likely) lead to
>> instability,
>> especially with Parrinello-Rahman.
>
>I carried out independent NPT processes with different tau_p values = 1.5,
>1.0 and 0.5
>
>
>
>## tau_p 1.5
>Energy Average Err.Est. RMSD Tot-Drift
>-------------------------------------------------------------------------------
>Pressure 2.62859 2.6 185.68 2.67572 (bar)
>
>
>## tau_p 1.0
>Energy Average Err.Est. RMSD Tot-Drift
>-------------------------------------------------------------------------------
>Pressure 0.886769 1.7 187.737 0.739 (bar)
>
>
>
>## tau_p 0.5
>Energy Average Err.Est. RMSD Tot-Drift
>-------------------------------------------------------------------------------
>Pressure 2.39911 2.2 185.708 6.8189 (bar)
>
>##############################
>
>It is clear that when tau_p =1.0, average pressure of the system (=0.89
>bar) is close to ref_p =1.0 bar
>However, it is unclear to me as to how to assign a good value to tau_p in
>order to reach at a close value of ref_p. As shown above, both of the
>average pressures as tau_p =1.5 and 0.5 are much higher than that as tau_p
>=1.0. A smaller tau_p may or may not help.
>
>
>Another issue caused by system pressure is about pbc box size. Since I use
>pressure coupling, the box size is not fixed such that protein moved away
>the center of membrane for a long simulation like 30 ns. Box size changes
>significantly during production MD. Is there a way to fix the box size at
>the very beginning ? although turning off pressure coupling will make box
>size fixed.
>
>Best regards,
>
>Dwey
>
>
>
>
>--
>View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011137.html
>Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
>------------------------------
>
>Message: 2
>Date: Thu, 12 Sep 2013 11:33:23 +0800 (CST)
>From: aixintiankong <aixintiankong at 126.com>
>Subject: [gmx-users] how to make a index file
>To: gmx-users at gromacs.org
>Message-ID:
> <197e2244.116e1.141103afe09.Coremail.aixintiankong at 126.com>
>Content-Type: text/plain; charset=GBK
>
> i want to analyze the change of secondary structure of the mainchian frome residue 20 to residue 60. so i want to make a index file that only contain the maninchian+H from residue 20 to residue 60. i have inputed the command " make_ndx -f em.pdb -o index.ndx", but i don't kown how to do next . what should i input ? thank you very much!
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 12 Sep 2013 04:12:34 +0000
>From: Dallas Warren <Dallas.Warren at monash.edu>
>Subject: RE: [gmx-users] RE: average pressure of a system
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
> <F625AF4746B3A74DACFF00F6F65BECCBAA760675 at PRK-MBX-04.vcp.local>
>Content-Type: text/plain; charset=utf-8
>
>> I carried out independent NPT processes with different tau_p values =
>> 1.5,
>> 1.0 and 0.5
>>
>>
>>
>> ## tau_p 1.5
>> Energy Average Err.Est. RMSD Tot-Drift
>> -----------------------------------------------------------------------
>> --------
>> Pressure 2.62859 2.6 185.68 2.67572
>> (bar)
>>
>>
>> ## tau_p 1.0
>> Energy Average Err.Est. RMSD Tot-Drift
>> -----------------------------------------------------------------------
>> --------
>> Pressure 0.886769 1.7 187.737 0.739
>> (bar)
>>
>>
>>
>> ## tau_p 0.5
>> Energy Average Err.Est. RMSD Tot-Drift
>> -----------------------------------------------------------------------
>> --------
>> Pressure 2.39911 2.2 185.708 6.8189
>> (bar)
>>
>> ##############################
>>
>> It is clear that when tau_p =1.0, average pressure of the system
>> (=0.89
>> bar) is close to ref_p =1.0 bar
>> However, it is unclear to me as to how to assign a good value to tau_p
>> in
>> order to reach at a close value of ref_p. As shown above, both of the
>> average pressures as tau_p =1.5 and 0.5 are much higher than that as
>> tau_p
>> =1.0. A smaller tau_p may or may not help.
>
>As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not statistically different. If you use that in a publication then any conclusions based on that will be rejected.
>
>To demonstrate to yourself how variable the pressure is, the tau_p=1 run, run the pressure analysis again using g_analyze, but using only the first half and the last half of the trajectory. You will find that the average values for both parts of the trajectory are not the same.
>
>> Another issue caused by system pressure is about pbc box size. Since I
>> use
>> pressure coupling, the box size is not fixed such that protein moved
>> away
>> the center of membrane for a long simulation like 30 ns. Box size
>
>That is not due to the pressure coupling. Motion of the protein within the box is simply due to diffusion etc. Also remember, that you have in effect an infinite repeating box in all directions, so the "center" of the box is arbitrary. If you want the protein to remain in the center for visualisation purposes, then you do post processing on the box using trjconv.
>
>> changes
>> significantly during production MD. Is there a way to fix the box size
>> at
>> the very beginning ? although turning off pressure coupling will make
>> box
>> size fixed.
>
>If you want fixed box dimensions / volume then you perform NVT. But that will not help with either issues above.
>
>The problem here is you are trying to make comparisons in the behaviour of simulations where there will not be a statistically significant difference in the property you are adjusting. Any differences you observe are more than likely going to be due to chance, rather than pressure.
>
>Catch ya,
>
>Dr. Dallas Warren
>Drug Delivery, Disposition and Dynamics
>Monash Institute of Pharmaceutical Sciences, Monash University
>381 Royal Parade, Parkville VIC 3052
>dallas.warren at monash.edu
>+61 3 9903 9304
>---------------------------------
>When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>------------------------------
>
>Message: 4
>Date: Thu, 12 Sep 2013 08:40:02 +0200
>From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>Subject: Re: [gmx-users] RE: average pressure of a system
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
> <CABzE1SiQ7=hhi25iZwYjX3SDjLSkxtyMJBcBD+3ey=D6Pd44yQ at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi Dallas, Justin, e.a.,
>
>As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not
>> statistically different.
>>
>
>This is not true. Whether this is statistically different depends on the
>number of independent samples. For pressure, the fluctuations are wild, and
>the autocorrelation is low, so for a reasonable length simulation you'll be
>able to get sufficient samples to mark a small difference like that as
>statistically significant. Whether it is physically significant is quite a
>different matter.
>
>Cheers,
>
>Tsjerk
>
>
>------------------------------
>
>Message: 5
>Date: Thu, 12 Sep 2013 11:31:05 +0200
>From: "Patrick Onck" <p.r.onck at rug.nl>
>Subject: [gmx-users] PhD vacancy on MD modelling at University of
> Groningen
>To: <gmx-users at gromacs.org>
>Message-ID: <D62C099311B74E8B99EC7620A738DCBC at mm20>
>Content-Type: text/plain; format=flowed; charset="iso-8859-1";
> reply-type=original
>
>Dear all,
>
>A four-year computational Ph.D. position on "MD modelling of unfolded
>proteins in aging nuclear pores" is available at the University of
>Groningen, The Netherlands. For details, see
>
>http://imechanica.org/node/15081
>
>For applications contact Prof.dr.ir. P.R. Onck at p.r.onck at rug.nl.
>
>Sincerely, Patrick Onck
>=======
>Prof.dr.ir. P.R. Onck
>University of Groningen
>Zernike Institute for Advanced Materials
>Applied Physics, Micromechanics of Materials group
>Nijenborgh 4
>9747AG Groningen
>The Netherlands
>Tel. +31(0)503638039
>http://www.rug.nl/staff/p.r.onck/index
>=======
>
>
>
>------------------------------
>
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