[gmx-users] Re: gmx-users Digest, Vol 61, Issue 22

[Jacek Czub]

zawieszla sie jeszcze szmaciarz?

gmx-users-request at gromacs.org wrote:
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> Today's Topics:
>
>    1. Re: P-coupling in vacuum, inflexibility (Pavel Semenyuk)
>    2. Recentering box after simulation of self-assembly of a
>       bilayer (maria goranovic)
>    3. Re: Recentering box after simulation of self-assembly	of a
>       bilayer (Justin A. Lemkul)
>    4. RE: Re:  v-rescale - harmonic oscillator (Berk Hess)
>    5. Re: atom name O3PB not found in residue ATP 340	while
>       generating exclusions when running pdb2gmx (TJ Piggot)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 7 May 2009 15:20:31 +0400
> From: "Pavel Semenyuk" <psemenyuk at belozersky.msu.ru>
> Subject: Re: [gmx-users] P-coupling in vacuum, inflexibility
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20090507110723.M89069 at belozersky.msu.ru>
> Content-Type: text/plain;	charset=koi8-r
>
> Thank you for answer.
> I checked up my .gro and .top files, and even I make it from pdb using pdb2gmx,
> simulation crashes. But without constraints or with all-bonds constraint, it work
> finely. But all-angles constraint results warnings (no p-coupling):
> --
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 21018.706436, max 77109.148438 (between atoms 1161 and 1162)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>       1      2   31.6    4.4548 104.4365      0.2401
>    1595   1597  177.4    0.3032   0.1406      0.2522
>    1594   1596  169.8    0.2330   0.4373      0.2522
> --
> Thank you..
>
> Best regards,
> Pavel I. Semenyuk
>
> On Wed, 6 May 2009 21:44:00 +0200, Tsjerk Wassenaar wrote
>   
>> Hi Pavel,
>>
>> It seems that your molecules are broken over the periodic boundaries.
>> Make sure that you set up your coordinates and topology file
>> correctly.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2009/5/6 Pavel Semenyuk <psemenyuk at belozersky.msu.ru>:
>>     
>>> Dear colleagues,
>>>
>>> I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for it a very
>>> big box, put my molecules into this box (without water) and then do simulations with
>>> pressure coupling to make my box smaller. So, how can I make my molecules inflexible? if
>>> I set links or shake constraints, it results too many warnings ("Warning: 1-4
>>> interaction between 12 and 33 at distance 30.841 which is larger than the 1-4 table size
>>> 2.400 nm").
>>> Thank you...
>>>
>>> Best regards,
>>> Pavel I. Semenyuk
>>>
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>>>       
>> -- 
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
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>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 7 May 2009 13:35:15 +0200
> From: maria goranovic <mariagoranovic at gmail.com>
> Subject: [gmx-users] Recentering box after simulation of self-assembly
> 	of a	bilayer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<9024f1330905070435g29e0da92r2d59bc0150dfaa90 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Please help !
>
> I ran a simulation of self-assembly of a DPPC lipid bilayer. At the end of
> the simulation, I have a bilayer, but it is not at the center of the box.
> Instead, it has two leaflets on each edge of the box separated by water,
> with the bilayer normal along the x-axis. How can I realign this trajectory,
> so that I can get the bilayer at the center of the box? It will also be nice
> to be able to align the membrane with the z-axis as is the norm. I have
> trialled and errored with many combinations of trjconv, but none seems to
> work
>
>   

-- 
Jacek Czub, Ph.D.
Department of Theoretical and Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11, 37077 Göttingen, Germany
phone: +49(551)201-2323 fax: +49(551)201-2302