From: Maryam X (maryamolagunju_at_gmail.com)
Date: Tue Jul 23 2019 - 10:34:18 CDT

Dear alex,
 
Sorry about that, i will do that henceforth.

Sent from my iPhone

> On 22. Jul 2019, at 17:47, Philippe Bopp <philippebopp_at_yahoo.com> wrote:
>
> Hi Maryam
>
> please remember that VMD is just a graphics tool, it knows nothing about "bonds",
> just some criteria (usually distances) when to draw lines between atoms
>
>> I have a system of 10 monomers in a simulation box trying to study aggregation and I ran my simulation using gromacs.
>> However, after the simulation, I noticed that I have periodic boundary conditions i.e. some of my molecules were broken and I >also noticed some unwanted bonds/lines showing when I play the trajectory movie in VMD.
>
> This could have several reasons, among which
>
> (I) your interactions potentials are no good and you have indeed in your configurations
> distances that VMD 'believes' (according to its criteria) to be 'bonds'
>
> (II) the periodic box assumed by VMD (parallelepipedic suppose) is not the correct one,
> i.e. when particles are 'box-shifted' (e.g. by wrap/unwrap) too short distances occur
>
> (III) probably more, eventually depending on input format (xyz, ......)
>
>> I have tried to solve the issue using trjconv (gromacs) but its not fixed.
>> I also read through the Vmd mailing list and followed the instructions I found but the problem persists. Can someone please help?
>
> compute quickly some g(r) (with and without pbc) and see whether you find anything suspicious
>
>
>> I will list the commands I have tried thus far below using vmd:
>> Pbc unwrap (this removed the bonds and made the protein whole but the the protein went out of the box)
>
> this is OK, which coordinates are stored in a trajectory (eg. all in box, grouped by neutral entiries ....)
> depends on your simulation code
>
>> Pbc wrap -compound -all (to move the proteins back inside the box), butv this did not completely solve the problem.
>> I have also tried
>> pbc wrap -center com -centersel "protein and chain A" -compound residue -all
>> pbc wrap -center com -centersel "protein " -compound residue -all
>
> except for these 'bonds', which mean nothing, is there anything else suspicious in your configuration?
>
> hope this helps
>
> Philippe