VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Mon Mar 02 2015 - 02:06:24 CST

Hi Norman

puts "Input) Molid?"

gets stdin *mid*

puts "Input) Centersel?"

gets stdin *comseltext*

Can you please tell me about *mid* and *comseltext*? what should be the
input for these two?
I want to try your method, as I really need to get the system back to
inside the box!

Thanks

On Wed, Nov 12, 2014 at 5:15 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Josh Vermaas
> *Gesendet:* Mittwoch, 12. November 2014 01:23
> *An:* M K
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Betreff:* Re: vmd-l: Protein went out of the Box
>
>
>
> Yup, because you told it to center the box on the moving protein, and only
> apply pbc corrections to the protein part, so PBCtools happily did nothing.
> What I think you want to do (assuming you have no interest in measuring the
> diffusion), is to move the entire system so that the protein's center is at
> the origin, and then rewrap it (if desired) so that the solvent molecules
> are on all sides of the polymer. The rmsdtrajectory tool has a nice
> interface for
>
> O_o Oh careful here, you CANT use the rmsdtrajectorytool BEFORE wrapping
> as it does also rotate. Using an rmsd alignment destroys every relation to
> the periodic cell!!! A better way is to write a script that moves the
> center of mass to the cells center using only translations, afterwards just
> wrap.
>
> Example:
>
> puts "Input) Molid?"
>
> gets stdin mid
>
> puts "Input) Centersel?"
>
> gets stdin comseltext
>
>
>
> set frames [molinfo $mid get numframes]
>
> set all [atomselect top all]
>
> set comsel [atomselect top ($comseltext)]
>
>
>
> for {set i 0} {$i < $frames} {incr i} {
>
> $all frame $i
>
> $all update
>
> $comsel frame $i
>
> $comsel update
>
>
>
> set com [measure center $comsel weight mass ]
>
> set lat [molinfo $mid get {a b c}]
>
> set shift [vecsub [vecscale $lat 0.5] $com]
>
>
>
> $all moveby $shift
>
> }
>
> puts "Info) Done!"
>
>
>
> Afterwards:
>
>
>
> pbc wrap –all –compoud res
>
>
>
> this.
>
> -Josh Vermaas
>
> On 11/11/2014 06:12 PM, M K wrote:
>
> 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
>
>
>
>
>
>
>
>
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