[gmx-users] Troubles with genbox and random insertion

[Ran Friedman]

Dear Shay,

Use the -seed flag

Ran.

Shay Amram wrote:
>
> Dear Gromacs users
>
>  
>
> I'm having a bit of a trouble with genbox: I want to insert 4 PLM
> (palmitate) molecules at random positions in my simulation.
>
> So I tried running:
>
> */genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 4PLM_tim.gro -seed 100/*
>
> */pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p --ter/*
>
> */ /*
>
> I got a GRO file and indeed there were 4 PLM molecules.
>
> _When I ran the same script again, I got the *exact* same GRO file._
> Meaning, the positioning of the PLM molecules wasn't truly random.
>
>  
>
> After reading the Description on
>
> http://www.gromacs.org/documentation/reference/online/genbox.html
>
> I saw that the --ci flag supposedly works only if I insert one molecule.
>
>  
>
> So I tried a different approach -- to add a single PLM four times like so:
>
> */# Palmitate No.1/*
>
> */genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro/*
>
> */pdb2gmx -f 1PLM_tim.gro -o 1PLM_tim.gro -p -ter/*
>
> */ /*
>
> */# Palmitate No.2/*
>
> */genbox -cp 1PLM_tim.gro -ci plm.gro -nmol 1 -o 2PLM_tim.gro/*
>
> */pdb2gmx -f 2PLM_tim.gro -o 2PLM_tim.gro -p -ter/*
>
> */ /*
>
> */# Palmitate No.3/*
>
> */genbox -cp 2PLM_tim.gro -ci plm.gro -nmol 1 -o 3PLM_tim.gro/*
>
> */pdb2gmx -f 3PLM_tim.gro -o 3PLM_tim.gro -p -ter/*
>
> */ /*
>
> */# Palmitate No.4/*
>
> */genbox -cp 3PLM_tim.gro -ci plm.gro -nmol 1 -o 4PLM_tim.gro/*
>
> */pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p --ter/*
>
> */ /*
>
> I got a different GRO than the one I got when adding the whole 4 of
> PLM in one line,
>
> but still, If I run the same batch of commands again, I get the same
> GRO file.
>
> If I run the first batch 50 times, each time I'll get the same GRO
> file as before.  Same is true for the second batch. Meaning the
> positioning is not random.
>
>  
>
> I tried fiddling with it some more (removing "-seed 100" etc., ) and
> still the result is the same.
>
>  
>
> Thank you very much in advance and best regards,
>
> Shay Amram
>


-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
------------------------------------------------------

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