[gmx-users] trjconv -pbc nojump

[Reisser, Sabine (IPC)]

Well, in the end I would like to have an average value for the P atoms of each leaflet. I know which lipids belong to which leaflet, but I need to avoid box jumps along z, otherwise I will obviously get a wrong average.
Using first trjconv  -pbc whole and then -pbc nojump actually seems to work in the way that molecules don't jump in z anymore. However, they are not whole anymore. 
Also, I would like all lipids of one leaflet on one side of the box. Now, the lipids upper edge is at the box edge, and some have jumped to the lower box edge. I thought maybe with -pbc cluster I could fix this. Otherwise I have to shift the molecules which are jumped (already in the starting structure) manually by the box height.

Cheers
Sabine

--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology


________________________________________
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von Justin Lemkul <jalemkul at vt.edu>
Gesendet: Mittwoch, 2. September 2015 15:06
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote:
> Thanks, I made them whole and tried to cluster the lipids with -pbc cluster.
> However, I keep getting a Fatal error:
> Molecule 1 marked for clustering but not atom 1 in it - check your index!
>
> This happens no matter which index group I use.
> Do you have any ideas what's the reason?
>

Does it even make sense to try to cluster these molecules?  Note that not every
step on that list is needed.

-Justin

> Cheers
> Sabine
>
>
> --
> Dr. Sabine Reißer
> Theoretical Chemical Biology
> Institute of Physical Chemistry
> Karlsruhe Institute of Technology
>
>
> ________________________________________
> Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von Justin Lemkul <jalemkul at vt.edu>
> Gesendet: Mittwoch, 2. September 2015 14:13
> An: gmx-users at gromacs.org
> Betreff: Re: [gmx-users] trjconv -pbc nojump
>
> On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote:
>> Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete.
>>
>
> Making molecules whole should be the first step, followed by removing jumps.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>
> -Justin
>
>> Cheers
>> Sabine
>>
>>
>>
>> --
>> Dr. Sabine Reißer
>> Theoretical Chemical Biology
>> Institute of Physical Chemistry
>> Karlsruhe Institute of Technology
>>
>>
>> ________________________________________
>> Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> im Auftrag von Ganesh Shahane <ganesh7shahane at gmail.com>
>> Gesendet: Mittwoch, 2. September 2015 12:19
>> An: gmx-users at gromacs.org
>> Betreff: Re: [gmx-users] trjconv -pbc nojump
>>
>> Hi Reisser,
>>
>> Instead of using -pbc nojump, use -pbc whole.
>>
>> On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
>> sabine.reisser at kit.edu> wrote:
>>
>>> Hi,
>>>
>>>
>>> I want to use trjconv -pbc nojump to create a trajectory without box
>>> jumping of molecules. The molecules (lipids) also start to diffuse out of
>>> the box like they should, but in some a part of the molecule still jumps
>>> (as I could observe in xy direction), while the rest doesn't, leading to
>>> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
>>> file in the -s option, or a gro file (with only complete molecules), same
>>> result.
>>>
>>>
>>> I'd be glad if somebody could give me a hint.
>>>
>>>
>>> Cheers
>>>
>>> Sabine
>>>
>>>
>>>
>>> --
>>> Dr. Sabine Reißer
>>> Theoretical Chemical Biology
>>> Institute of Physical Chemistry
>>> Karlsruhe Institute of Technology
>>>
>>> --
>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>> Best Regards,
>> Ganesh Shahane
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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