[gmx-users] Troubles with genbox and random insertion

[Shay Amram]

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

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