Re: about long namd trajectory and pbc effect

From: Liqun Zhang (lxz79_at_case.edu)
Date: Mon Dec 03 2012 - 14:00:50 CST

Thanks a lot! My problem was solved after using pbc wrap command as
suggested. I will calculate the interaction between protein and water using
charmm codes based on the new trajectory.

lqz

On Mon, Dec 3, 2012 at 1:44 AM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

> Why not simply wrap with „–center com –centersel protein” ?****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Thomas Evangelidis
> *Gesendet:* Sonntag, 2. Dezember 2012 22:40
> *An:* Liqun Zhang
> *Cc:* namd-l_at_ks.uiuc.edu
> *Betreff:* Re: namd-l: about long namd trajectory and pbc effect****
>
> ** **
>
> Hi Liqun,
>
> Actually this is a VMD question. If your analysis does not require the
> waters to be in contact to the part that sticks out of the cell you can
> simply use the atomselect macro "pbwithin" to select them. I.e.
>
> atomselect top "water pbwithin 5 of (protein and resid 1 to 20)"
>
> If your analysis requires wrapped water coordinates, then try the
> following in VMD Tk console:
>
> pbc wrap -all -parallelepiped -compound fragment -center bb -centersel
> protein
>
> If that does not surround the outliers with sufficient waters then you'll
> have to use a more drastic solution. I have written a VMD plugin that given
> a number of waters N (or other hetero compounds) finds the closest N
> waters to your protein and surrounds the whole protein with these N waters.
> Instead of the whole protein you can also restrict your analysis to a part
> of interest, e.g. the catalytic cleft. So I think this does exactly what
> you seek. The plugin is named Truncate Trajectory and you can find more
> info at:
>
>
> https://sites.google.com/site/thomasevangelidishomepage/truncate-trajectory-plugin-for-vmd
>
> If you need any further info then contact me directly.
>
> HTH,
> Thomas
>
>
>
> ****
>
> On 2 December 2012 22:53, Liqun Zhang <lxz79_at_case.edu> wrote:****
>
> Dear namd users:
>
> I have run a very long namd simulation for a protein complex (2 proteins
> binded) in a water box to observe the protein complex separation process.
> Because of the pbc effect, I unwrapped the simulation trajectory. So I no
> longer see one protein jumped at the edge of the box frequently. But the
> unwrapped trajectory showed part of the protein outside of the water box.
> Now I like to calculate the interaction between protein and the surrounding
> water. Since one protein is partially outside of the box, I can not select
> water around it. Then what I should do with that? Do I have to readjust the
> simulation trajectory? If yes, how to show waters around the protein
> outside of the box using pbc command in vmd? Any suggestion is welcomed.
> Thanks a lot.
>
> Best regards,
>
> lqz****
>
>
>
>
> -- ****
>
> ======================================================================****
>
> Thomas Evangelidis****
>
> PhD student****
>
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE****
>
> email: tevang_at_pharm.uoa.gr****
>
> tevang3_at_gmail.com****
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/****
>
> ** **
>
> ** **
>

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:49 CST