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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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