VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Jun 12 2015 - 11:20:26 CDT

Oh yeah. Take a look at the manual for pbc tools
(http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/). There needs to
be a -all argument, or it defaults to doing only the active frame
(usually the last one). pbctools gives you this flexibility so that you
can use it with things like bigdcd, where you only have one loaded frame
at a time.

-Josh

On 6/12/15 11:13 AM, Francesco Pietra wrote:
> I forgot to mention that the full recomposition of the system holds
> for the last frame 4999 only. Should the "painfully slow unwrap
> process" be used in order to run the movie of the simulation?
>
> ---------- Forwarded message ----------
> From: *Francesco Pietra* <chiendarret_at_gmail.com
> <mailto:chiendarret_at_gmail.com>>
> Date: Fri, Jun 12, 2015 at 5:53 PM
> Subject: Re: vmd-l: unwap/wrap failure in recomposing splitted system
> from periodic cells
> To: Josh Vermaas <vermaas2_at_illinois.edu <mailto:vermaas2_at_illinois.edu>>
> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>>
>
>
> Hi Josh:
>
> I tried again, hitting gold.
>
> Looking better at the end of the simulation, I noticed that the
> tetramer had now been separated into two dimers. On one side of the
> box, PRD half out the box and PRB entirely within the box. At the
> opposite side, PRA nearly totally out of the box and PRC entirely
> within the box.
>
> Repeating your commands with *segname PRC", I got the whole system
> perfectly in orde, including all ligands and potential ligands, within
> the same box.
>
> I can safely rule out errors from my side in my previous failed attempts.
>
> No words enough to thank you.
> francesco
>
> PS: Do you have any idea whether that could be extended to bigdcd in
> order to follow certain specific rgyr along the whole trajectory?
> (with 64GB at the computing center I am limited to load three 24h
> simulations)
>
> On Fri, Jun 12, 2015 at 4:47 PM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> Hmm... In principle it shoulda totally worked, but you can try
> things like removing the -sel all argument? Admittedly I was going
> on memory, so maybe there is something weird about all not being
> in quotes. I like how it complains about an unknown option after
> having used it the previous command.
> -Josh
>
>
> On 6/12/15 2:33 AM, Francesco Pietra wrote:
>> Hi Josh:
>>
>> With "segname PRA" in place of your "segname A", for the same
>> purpose,
>>
>> Main console display active (Tcl8.5.6 / Tk8.5.6)
>> (MD_O2-out) 1% pbc wrap -sel "protein" -centersel "segname PRA"
>> -center com -compound fragment
>> Info) 100.0% complete (frame 4999)
>> >main< (MD_O2-out) 2 % pbc wrap -sel all -centersel "protein"
>> -center com -compound fragment
>> error; pbcwrap: unknown option: -compound
>> >Main< (Md_O2-out) 3 %
>>
>> Is that understandable why error?
>>
>> Thanks a lot
>> francesco
>>
>> On Thu, Jun 11, 2015 at 9:31 PM, Josh Vermaas
>> <vermaas2_at_illinois.edu <mailto:vermaas2_at_illinois.edu>> wrote:
>>
>> Here is how I do it on my own systems, which avoid the
>> painfully slow unwrap process:
>>
>> pbc wrap -sel "protein" -centersel "segname A" -center com
>> -compound fragment
>> pbc wrap -sel all -centersel "protein" -center com -compound
>> fragment
>>
>> The trick here is that I have one monomer (segname A) that I
>> use to bring the other potentially split monomers into the
>> same pbc box. The unwrap command followed by a wrap would
>> also work, but you forgot the "compound fragment" argument,
>> so the algorithm did what you told it to, and that is to wrap
>> atoms around into a rectangle regardless of connectivity,
>> resulting in ludicrously long bonds.
>> -Josh Vermaas
>>
>>
>> On 6/11/15 12:24 PM, Francesco Pietra wrote:
>>> Hello:
>>>
>>> Following the splitting of a homotetramer into intact
>>> trimer/monomer at ca 300 ns trajectory, I tried the
>>> following three commands in the tk console of the remote
>>> visualization for the last 24h simulation (ca 11 GB file
>>> size). I had 64GB memory available (the max I could have)
>>>
>>> set all [atomselect top all]
>>>
>>> pbc unwrap -sel all (which operated very slowly on the 4999
>>> frames)
>>>
>>> pbc wrap -sel all
>>>
>>> The latter created a box of lines of the original size.
>>> Then, command "all not water" removed those pertaining to
>>> water, leaving lines not amenable to any "Drawing Method".
>>> These lines looked like long bonds, which were not present
>>> in the splitted system.
>>>
>>> I used "all" as the system is also composed of ligands, some
>>> firmly residing into binding pockets, some other ones
>>> traveling from the surrounding medium to their binding pockets.
>>>
>>> The "intact" in the first line above is not entirely
>>> correct. That is, the monomer is removed from the
>>> homotetramer without its major ligand (the substrate to be
>>> modified by the enzyme).
>>>
>>> Thanks for suggestions about how to amend my faulty commands.
>>>
>>> francesco pietra
>>
>>
>
>
>