VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Tue Nov 11 2014 - 22:46:57 CST

Thank you Tristan. This also didn't work. Nothing happens. Noteworthy to
mention that the simulation has 8862 fragments.

On Wed, Nov 12, 2014 at 12:28 PM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:

> You need to include the switch:
>
>
>
> -compound fragment
>
>
>
> In there. This will force it to wrap your entire polymer as a single unit.
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *M K
> *Sent:* Wednesday, 12 November 2014 10:13 AM
> *To:* Josh Vermaas
> *Cc:* Vy Phan; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Protein went out of the Box
>
>
>
> Hi,
>
> I face a similar problem.
>
> I simulate a polymer chain in water. I can select this chain using
> "protein" selection. During the simulation, it moves and goes beyond the
> boundaries of the box, and enters from the other side due to the periodic
> nature.
>
> I want to keep this polymer chain always in the center of the cubic box; a
> good try is probably keeping the center of mass of the polymer chain in the
> center of the box. I tried the following code and some other variations,
> but they don't work; the chain is again split into parts when going beyond
> the boundaries:
>
> *pbc wrap -all -sel "protein" -center boundingbox -centersel "protein"*
>
> Can someone please help? What is the problem with the code I'm using?
>
>
>
> On Tue, Sep 30, 2014 at 12:14 AM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
> Hi Phan,
>
> You can use the PBCtools plugin (
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/) to rewrap your
> trajectory. If you just care about the hydrogen bonds between proteins,
> what you should be able to do is use something like this:
>
> pbc wrap -all -sel "protein" -center com -centersel "some atomselection
> text that only picks out one of the two protein copies"
>
> Then the selected protein will be near the center, and any of the atoms
> involved in hydrogen bonding should be inside the same unit cell. Read the
> documentation, and play around to see which combination of options you
> prefer.
>
> -Josh Vermaas
>
>
>
> On 09/29/2014 08:09 AM, Vy Phan wrote:
>
> Dear Vmd users,
>
> My systems for MD simulations included 2 protein, but after 50ns of
> trajectory, one protein go out side the water box (sometimes comeback). I
> knew why this phenomenon happened but when I do not know how to analyze the
> result.
>
> I have problem when I calculated hydrogen bonds between two protein.
> Because of the boundary condition, the result of hydrogen bonds is not
> right. How can I solve this problem?
>
> Thank a lot and best regards,
>
> Phan Vy
>
>
>
>
>