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-requ...@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 <mpi...@gmail.com>
>Subject: [gmx-users] RE: average pressure of a system
>To: gmx-users@gromacs.org
>Message-ID: <1378956710192-5011137.p...@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 <aixintiank...@126.com>
>Subject: [gmx-users] how to make a index file
>To: gmx-users@gromacs.org
>Message-ID:
> <197e2244.116e1.141103afe09.coremail.aixintiank...@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.war...@monash.edu>
>Subject: RE: [gmx-users] RE: average pressure of a system
>To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>Message-ID:
> <f625af4746b3a74dacff00f6f65beccbaa760...@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.war...@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 <tsje...@gmail.com>
>Subject: Re: [gmx-users] RE: average pressure of a system
>To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>Message-ID:
> <CABzE1SiQ7=hhi25iZwYjX3SDjLSkxtyMJBcBD+3ey=d6pd4...@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.o...@rug.nl>
>Subject: [gmx-users] PhD vacancy on MD modelling at University of
> Groningen
>To: <gmx-users@gromacs.org>
>Message-ID: <D62C099311B74E8B99EC7620A738DCBC@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.o...@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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