[gmx-users] Editing of the existing system

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 31 14:27:57 CEST 2012

James Starlight wrote:
> Mark,
> I've forced with some problems during MDrun of such system with the two 
> proteins.
> Firstly, after addition of second protein, I've removed all water and 
> ions and solvated my system with genbox and genion.
> Than I've redefined groups of my proteins ( wich are like a_1-4000 and 
> a_4001-5000 ) in index.ndx file in the separate T_coupl, COM and 
> energygroups because atom order was perturbed after solvation.

Separate COM motion removal groups are tricky.  I'm still not completely clear 
on what your system looks like, but if you've got two proteins in two layers of 
solvent and you expect one or both of them to move in such a way that they begin 
to interact, it may not be appropriate to be using the groups you've shown below.

> Than I've minimized my system  with the Emtool=500

And what was the exact outcome?

> The problems were on the nvt equilibration phase with the posres applied 
> on the both proteins. I have no errors, notes or warninngs from GROMPP 
> but when I've started my simulation with MDrun my system was crushed on 
> the 1st step with the multiple LINKS warnings as well as message that 
> something wrong with interactions between 1st protein atoms and 
> surrounded water ( as I've said previously after addition of the second 
> protein to my system I've resolvated my system again).

Please don't attempt to interpret the error message.  Copy and paste the actual 
output (not the LINCS warnings themselves, we all know what those look like).

> Might my system be not properly minimized  or does something wrong else 
> in addition?

That depends on your answers to the questions posed above.  You should also 
provide a complete .mdp file.  If the system crashes on the very first step, 
either minimization was insufficient or your .mdp parameters break the 
underlying physical model and cause an immediate collapse.


> James
> 31 марта 2012 г. 2:20 пользователь Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> написал:
>     On 31/03/2012 1:00 AM, James Starlight wrote:
>>     Mark,
>>     Also I'd like to know some more about most correct parametrisation
>>     of such new edited system. My new system consist of two proteins (
>>     one- wich was initially and the second small peptide wich I've
>>     docked to the first protein). So now I need to define 2 separate
>>     groups for the below enties of my MD files
>>     |energygrps = Protein peptide
>>     |
>>     tc-grps     = Protein_Bilayer SOL_ions_peptide
>>     and finally CoM groups because of the general anisotropy of the membrane system
>>     comm-grps	= Protein_Bilayer SOL_Ions_Peptide
>>     I've made itp file for the peptide via pdb2gmx so in th default definition both the protein and peptide are the protein enty in the index file.
>>     I've separate both of the protein and peptide by selection of two subsets of atoms wich represent to the each of that enties.
>>     So finally I have two groups in the index.ndx file
>>     a_1-5000  ( it's protein)
>>     a_9999-10500 (it's peptide)
>     You can use make_ndx (or a text editor on the .ndx file) to give
>     them more helpful names.
>>     Does this separation correct in general ? I have some fears because both protein and peptide consist of the same residue numbers in the GRO file ( e.g there are 212- lys wich is part of the protein and 212-Pro wich is part of the peptide ) Might this system be tended to errors?
>     Residue numbers are largely irrelevant. pdb2gmx and maybe grompp use
>     them for matching a coordinate file to the .rtp and .top
>     (respectively), but only really in the sense that the number changes
>     from one residue to another.
>>     I have no errors during processing of that sustem by grompp as well as md run. What should I do for such system consisted of two proteins in separate phases ( membrane-like and water)
>>     ?
>     All seems basically sound.
>     Mark
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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