Re: how to fix the problem

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Fri Nov 14 2014 - 20:02:44 CST

Oops, I meant "$sel moveby $vector".

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Fri, Nov 14, 2014 at 8:02 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Hi LQZ,
>
> If you don't like where the pbc join put the protein, just shift it
> where you would like it by a cell basis vector (using $sel move
> $vector). Shifting by a cell basis vector or any linear combination of
> cell basis vectors with integer coefficients doesn't change the system
> physically.
>
> Forgive me if you already understand this, but I should point out that
> various pbctools commands only change how the system looks and don't
> change it in any physically meaningful way. In general, how you wrap
> your structure doesn't matter to NAMD. For example, even if VMD makes
> it look like a bond crosses almost the entire system except for 2
> angstroms, NAMD considers only the minimum distance between two
> periodic images, which is just 2 angstroms apart.
>
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
>
> On Fri, Nov 14, 2014 at 5:19 PM, Liqun Zhang <lxz79_at_case.edu> wrote:
>> Dear all:
>>
>> I have run a simulation for a protein in lipid system for a very long time.
>> In order to remove the pbc effect, I unwrapped the trajectory for protein
>> and the lipids using pbc commands in vmd program, which made part of the
>> protein broken in the z-direction. But when I tried to use join command to
>> join the broken part to the major part of the protein, the major part of the
>> protein instead was shifted to the broken part. I am not sure how to solve
>> the problem. Can I get some suggestion here? Thank you very much.
>>
>> Best,
>>
>> LQZ

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