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Re: [lammps-users] VDW radius of TIP3P
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Re: [lammps-users] VDW radius of TIP3P

From: Steve Plimpton <sjplimp@...24...>
Date: Sat, 28 Oct 2017 07:40:41 -0600

Your workflow to build a hybrid system is not very clear.
I suggest you build it one step at a time, and visualize
what each tool is doing in separate files.  To insure
atoms are where you want them.  Then merge
them one step at a time and re-do more viz.


On Fri, Oct 13, 2017 at 2:00 PM, Neda Rafiee via lammps-users <> wrote:
Dear users,
I have a psf file for lipid bilayer from charmm-gui.  I changed my system and after that to convert it into lammps input files, I used the following command to add water to my system:
Perl   all36_lipid   -lx =7  -ly=7   -lz=20   -water  

Then I noticed many water molecules inserted in my lipid bilayer while they should not be there. What do you suggest me to do to remove these unwanted water molecules? 
I have also read that these unwanted waters will escape from within the bilayer after the equilibration but actually after 200 ps of npt equilibration, not only  the water molecules still exist, but also two layers of lipid are geting separated from each other !
I new in gromacs, we can solve this problem by increasing the VDW radius of carbon atoms of lipid molecules just temporarily for solvating the system, but how can I do the same procedure using the perl command line above? and in lammps, which file contains the VDW radius of carbon?
Any help is appreciated.

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