From: Felipe Merino (
Date: Wed Jun 10 2015 - 02:50:54 CDT

Hi Francesco,

Unfortunately I cannot help you with bigdcd since I have never used it
myself. Anyways, I have used before the pbctools from a text only
version of vmd to fix the wrapping of some protein/DNA complex
simulations before.

The script was something like this

package require pbctools

mol new ../Oct4_UTF1_ModelC.prmtop
for { set d 1 } { $d <= 20 } { incr d } {
         mol addfile restart.coor
         mol addfile ../Oct4_UTF1_ModelC_dyn$d.dcd waitfor all
         set macromol [ atomselect top "protein or nucleic" ]
         pbc unwrap -sel "protein or nucleic"
         set lFrame [ expr [ molinfo top get numframes ] -1 ]
         animate goto $lFrame
         animate write namdbin restart.coor
         animate write dcd $d.dcd beg 1 end $lFrame waitfor all sel
         animate delete beg 0 end $lFrame

In my case I only wanted the macromolecules and I did not write any
water or other things. The unwrapped restart file is necesary when you
unwrap several consecutive windows since otherwise vmd does not know
where to put the molecules.

I hope that helps



On 10/06/15 09:24, Francesco Pietra wrote:
> Hi Felipe:
> While I am still considering how to apply your suggestion to get
> everything (also ligands, either already into the protein or
> approaching it from the surrounding medium) in the system, do you have
> an idea how to apply bigdcd scripts (rmsd centermass rgyr distance,
> for example) under such "broken" conditions of the system?
> Given the size of the system, I am very limited in using graphical VMD
> at the computing center, so I shifted to text VMD with bigdcd (which
> worked nicely with "unbroken" system", while I have no idea whether
> pbc commands can be used "blindly" under text mode)
> thanks
> francesco
> On Tue, Jun 9, 2015 at 5:10 PM, Felipe Merino
> <
> <>> wrote:
> Hi,
> I remember that for this kind of problems you have to first unwrap
> the simulation (pbc unwrap -sel protein for example) and later
> re-wrap it around your protein. That should give you a unit cells
> centered around you intact tetramer.
> Best
> Felipe
> On 09/06/15 13:04, Francesco Pietra wrote:
>> Hello:
>> During NAMD MD with a large homotetramer, at ca 250ns a small
>> portion of the tetramer is out of the TIP3 box. At ca 300ns one
>> of the subunits splits out of the other three. It appears to be
>> an artifact of contiguous boxes, however the below command (VMD
>> 1.9.2 remote visualization from the computing center)) does not
>> recompose the homotetramer
>> pbc wrap -all -compound res -center com -centersel protein
>> pbc box
>> The additional complication is that I am monitoring ligands that
>> from the surrounding medium penetrate the cavities of the protein
>> to the active center occupied by the substrate.
>> Thanks for suggestion how to recompose the homotetraner
>> francescp pietra