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:* [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] <mailto:[EMAIL PROTECTED]> > Skype: ran.friedman > ------------------------------------------------------ > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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