[gmx-users] Troubles with genbox and random insertion

[Vasilii Artyukhov]

That's the whole idea, you _have_ to change the seed value, since it's used
by the program to generate a sequence of pseudorandom numbers...

2007/9/18, Shay Amram <shayamra at post.tau.ac.il>:
>
> 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
>
> Skype: ran.friedman
>
> ------------------------------------------------------
>
>
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