[gmx-users] about periodic image violations

[Justin A. Lemkul]

Anna Marabotti wrote:
> Sorry, I forgot to change the subject of my previous mail.
> Anna 
> 
> -----Messaggio originale-----
> Da: Anna Marabotti [mailto:anna.marabotti at isa.cnr.it] 
> Inviato: martedì 28 giugno 2011 12.09
> A: 'gmx-users at gromacs.org'
> Oggetto: R: gmx-users Digest, Vol 86, Issue 183
> 
> Dear Tsjerk, dear all,
> thank you very much for suggestion. One of the main reasons why I never used
> the rhombic dodecahedron box for my simulations is the fact that it is
> really hard to visualize the results with programs such as VMD or Pymol, and
> therefore I cannot check easily during the setting of my system if the work
> proceeds properly. Since I would like to redo my simulations following your
> suggestion, could you please give me some hints on how to proceed in order
> to visualize easily the system? For example, now I created a dodecahedric
> box filled with water and ions. I tried to visualize it with VMD and I saw
> it as a rectangular box with the protein at one edge. I tried to use the
> command trjconv:
> 
> trjconv -f prot_dod_box_neu.gro -s prot_dod_box_neu.tpr -o
> prot_dod_box_neu2.gro -pbc mol -ur compact
> 
> and I obtained an error message stating:
> Fatal error:
> Index[84328] 84329 is larger than the number of atoms in the trajectory file
> (84328)
> 
> I don't find this error neither in the gmx-users list archive (indeed it's
> becoming harder and harder to search into this archive, given that each
> message is visualized 10 times, as I already noticed sometimes ago), nor in
> the Error section. The first .gro file is the one coming from genion, and
> the .tpr file is the one I used to neutralize the system, which is the .tpr
> file I should give to trjconv? You see, if every time I try to use a box

They need to correspond to the same system.  Therefore, after the system is 
constructed (i.e. after genion in this case), create a new .tpr file.  Your 
command is otherwise correct.  Whether or not VMD then displays the proper unit 
cell shape is another matter.  If you display all of the solvent molecules, you 
should get a nice, pseudo-spherical shape, but if you visualize the box vectors 
then I think you'll still get a triclinic cell.  But that's a VMD thing, not a 
Gromacs thing :)

-Justin

> different from the standard cubic one I has to deal with such maybe trivial
> (for you) problems, but difficult and long to solve, I'm quite discouraged
> to use it! This is also a kind request for Gromacs Web site managers: could
> you please add a section for this (recurrent, I suspect) problem of box
> visualization in the "How-to" section? it would be very useful for users, I
> think, and probably also for you (less trivial questions posted to the
> gmx-users list...)
> 
> Many thanks in advance for the help you could provide me.
> Anna
> 
> 
> Message: 6
> Date: Mon, 27 Jun 2011 17:05:17 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] about periodic images violation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTim3r1339YB6ECKEDF9eTYRg+q+MqA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Anna,
> 
> The spikes you see occur because the protein is broken over the
> periodic boundaries. Not hard to see that a broken molecule will have
> a minimal minimal distance.
> 
> The other problem may well occur due to rotation of your molecule.
> Since you set -bt tric, you just get a rectangular unit cell, which
> has the drawback that the shortest distance may not be long enough to
> keep the protein from self-interactions in certain orientations. I
> know it's considered a pretty standard setup, which is why I mentioned
> it before. You should use a rhombic dodecahedron.
> 
> With a rectangular cell, you could even have self-interaction in a
> nastier way: the ends of the protein can try to avoid each other,
> rather than align with each other. That would result in an altered
> ensemble, yet one in which you wouldn't see violations of the minimal
> distance. In a rhombic dodecahedron the spatial distribution is much
> more uniform...
> 
> Cheers,
> 
> Tsjerk
> 
> On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti
> <anna.marabotti at isa.cnr.it> wrote:
>> Dear gmx-users,
>> I'm inserting into the discussion about periodic images since I'm
>> experimenting a problem of minimum distance violation too. I'm doing
>> simulations on a dimeric protein (with no covalent bonds between the two
>> subunits) which derives not from a crystallographic structure but from a
>> model. I made several simulations changing the gen_seed in order to
> explore
>> deeply the conformational space of the protein. I used a triclinic box
>> (option editconf -bt triclinic -d 1 -c) filled with spc water and
>> neutralized with ions; in my opinion, it's quite a standard system. I
>> equilibrated the system with a minimization (emtol = 500 reached) and with
>> NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched
> the
>> full MD for 30 ns, always at 310 K. I repeated this procedure
>> (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers),
>> starting from the same minimized structure. Obviously, in PR-NPT and full
> Md
>> simulations, I did not recalculated the initial velocity (it's a
>> continuation). Before starting with full MD I checked for energetic
>> parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no
>> apparent problems. I run the 30 ns simulations and now I'm checking for
> the
>> results.
>> Looking at the trajectories I see that in some (but not all) cases, the
>> protein moves from the center of the box to one of the edges, starting
> from
>> a time that is different in each simulation, when it happens. I run
>> g_mindist, and in some cases (generally when the protein doesn't move so
>> much) I see some "spikes" in the plot (that disappear if I apply trjconv
>> -pbc nojump to the trajectory), but apart from these "spikes" the minimum
>> periodic distance in the trajectory is at least 1.5 nm (I set van der
> Waals
>> cut-off at 1.4 nm). In other cases, however (essentially when the protein
>> starts moving towards the edges of the box), the minimum periodic distance
>> starts decreasing (in some simulations after 10 ns, in some simulations
>> after 20: there is not a common point after which you can see a sudden
>> decrease of minimum periodic distance of the system) and reaches a value
>> below 1.4 nm or even below 1 nm. Considering that the starting system is
>> more or less the same in all cases, I don't identify the reason why the
>> system "behaves" like this, and moreover what can I do to avoid this. My
>> questions are:
>> - do I have to enlarge the box? but I don't think that this would solve
> the
>> "motion" of the protein towards one edge of the box
>> - do I have to change the box? In his last message Tsjerk suggests to use
> a
>> rhombic dodecahedron box, could it be useful in my case?
>> - do you think it's a problem of stabilization of the system? Should I run
> a
>> deeper minimization, or a longer NVT+NPT in my system?
>> I'm quite puzzled especially because the system is the same in all cases,
>> the only thing I changed in my simulations is the gen_seed.
>> Could anybody give me some suggestions about it?
>> Thank you very much
>> Anna
>>
>>
>>
>>
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================