[gmx-users] Stopping protein jumping inside box

[Justin Lemkul]

On 2/13/13 8:47 AM, Naga Sundar wrote:
> Hi
>       Plz try  -pbc nojump option...It may work
>

Several iterations of trjconv are often needed to achieve the desired 
representation.  Indeed, the first step to removing jumps should be -pbc 
nojump...which removes jumps ;)

-Justin

> On Wed, Feb 13, 2013 at 5:29 AM, 라지브간디 <rajiv at kaist.ac.kr> wrote:
>
>> Dear gmx users,
>>
>>
>> I need to stop my protein jumping inside box. I have used  -pbc mol -ur
>> compact -center  command too but still the protein gets moving from one
>> place to other.
>>
>>
>> Could you please suggest me how to make the protein to stop in one place ?
>> Moreover, its protein with their ligand.
>>
>>
>>
>>
>> Thnx.
>>
>>
>>
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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