[gmx-users] RE: Stopping protein jumping inside box?

[vivek modi]

>
> Message: 1
> Date: Thu, 14 Feb 2013 14:13:03 +0900 (KST)
> From: ????? <rajiv at kaist.ac.kr>
> Subject: [gmx-users] RE: Stopping protein jumping inside box?
> To: gmx-users at gromacs.org,      gmx-users-request at gromacs.org
> Message-ID: <511c745f3fe9_ at _imoxion.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx,
>
> I've used -pbc nojump options but still the protein goes all around the box within 4ns. Any specific command to avoid this ? It's a myoglobin protein!

Try this command.

http://www.mail-archive.com/gmx-users@gromacs.org/msg13353.html


Regards,

-Vivek

> --------------------- orig.Message ---------------------
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> Sent date : 2013-02-14 07:24
> Subject : gmx-users Digest, Vol 106, Issue 69
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> Today's Topics:
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>    1. Stopping protein jumping inside box (?????)
>    2. Re: Stopping protein jumping inside box (Naga Sundar)
>    3. Re: Stopping protein jumping inside box (Justin Lemkul)
>    4. RE: on the ussage of SD1 integrator (Berk Hess)
>    5. Chandler autcorrelation function fitting (KARAKAS Esra)
>    6. Bond potential of atom groups (Steven Neumann)
>    7. Join my network on LinkedIn (Gideon Lapidoth via LinkedIn)
>    8. GROMOS54A8 parameters in GROMACS format (ABEL Stephane 175950)
>    9. Re: different springs - WHAM (Steven Neumann)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 13 Feb 2013 22:29:05 +0900 (KST)
> From: ????? <rajiv at kaist.ac.kr>
> Subject: [gmx-users] Stopping protein jumping inside box
> To: gmx-users at gromacs.org
> Message-ID: <511b98243fa7_ at _imoxion.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 13 Feb 2013 05:47:07 -0800
> From: Naga Sundar <naga25sundar at gmail.com>
> Subject: Re: [gmx-users] Stopping protein jumping inside box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CALobX4n_6hUoJhV-AEcjGj9UctvivV2H5U-+iZyVizmr0ECv6Q at mail.gmail.com>
> Content-Type: text/plain; charset=EUC-KR
>
> Hi
>      Plz try  -pbc nojump option...It may work
>
> On Wed, Feb 13, 2013 at 5:29 AM, ���������� <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.
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
>
> --
> Regards
> N.NagaSundaram
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 13 Feb 2013 08:50:04 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Stopping protein jumping inside box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <511B9A0C.9 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> 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, ��������������� <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.
>>>
>>>
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
> ------------------------------
>