[gmx-users] Troubles with genbox and random insertion

[Shay Amram]

Ah ok now I get it.

Thanks Ran, Thanks Vasilii.

 

-Shay

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From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Ran Friedman
Sent: Tuesday, September 18, 2007 15:35
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Troubles with genbox and random insertion

 

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

 

 

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