[gmx-users] Troubles with genbox and random insertion

[Ran Friedman]

If I understood you correctly, you wanted to have different random
orientations of the molecules around your protein. To get N different
orientations, you should run genbox N times with N different seeds.

Ran.

Shay Amram wrote:
>
> Greetings Ran,
>
> I tried to add the --seed flag as you said, at the end of each genbox
> (with different various numbers), and it doesn't help.
>
> (ran the following command:)
>
> */genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro --seed 4/*
>
>  
>
> Each time I change the number after "-seed" I get a different GRO file,
>
> But no matter how many time I run genbox with the same number after
> "-seed" I always get the same GRO file in the end.
>
>  
>
> Is it possible that there's something wrong in the system settings?
> Something that has to do with the way genbox chooses random numbers?
>
>  
>
> Thanks,
>
> -Shay
>
>  
>
>  
>
> ------------------------------------------------------------------------
>
> *From:* gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Ran Friedman
> *Sent:* Tuesday, September 18, 2007 14:40
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Troubles with genbox and random insertion
>
>  
>
> 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 <mailto:r.friedman at bioc.unizh.ch>
> Skype: ran.friedman
> ------------------------------------------------------
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php


-- 
------------------------------------------------------
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
------------------------------------------------------

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070918/19a319b2/attachment.html>