Re: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?
Hello Maria, You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) ) 2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline. Hope it will help Alok - Original Message - From: maria goranovic To: gmx-users@gromacs.org Sent: Sunday, October 21, 2007 3:57 PM Subject: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ? Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command: genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer. - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen -- ___ gmx-users mailing listgmx-users@gromacs.org 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___ gmx-users mailing listgmx-users@gromacs.org 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
[gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?
You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/ gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. Cleaner method is to: cp /usr/local/gromacs/share/top/vdwradii.dat ./vdwradii.dat and then modify the local file. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) ) Do I understand you to say that for you the gap does not completely dissapear in 500ps? Did you use semiisotropic coupling? Otherwise it will be more difficult for this space to fill in. It should fill in really quite quickly (500ps)... has for me. 2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline. I have previously posted such a script. It takes 10-30 minutes to run since it's not sophisticated, but it does work very well. http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html I forgot to mention that in the previously referenced script there is an assumption that you use a 3 atom water molecule. If you use tip4p then you would want if [ $count = 3 ]; then count=0 fi to be changed to: if [ $count = 4 ]; then count=0 fi and etc for tip5p. Hope it will help Alok - Original Message - Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command: genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer. - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ? Thank you -Maria ___ gmx-users mailing listgmx-users@gromacs.org 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
