[gmx-users] PR for CG lipid and CG protein

[chris.neale at utoronto.ca]

Dear Sunny,

I replied a while ago, but it seems to have not made it to the list.  
When using inflategro with gromacs3, you can run cycles like this:

1. inflategro.pl
2. mdrun (EM)
3. goto 1

When running with gromacs4, however, you must run cycles like this:

1. inflategro.pl
2. mdrun (EM)
3. trjconv -pbc mol
4. goto 1

since mdrun now writes broken molecules.

The developer of inflategro.pl, Christian Kandt, is aware of this and  
may have modified the script to allow broken molecules in inflategro,  
but if you have a version that is more than 2 months old then it  
certainly can not handle molecules that are broken over PBC, as lipids  
usually are near the boundary.

Chris.


On 1/8/10 7:30 PM, sunny mishra wrote:
> Hi All,
>
> I am trying to insert coarse grained protein to coarse grained lipid. My
> protein is CG 1SU4 and lipid is CG DPPC. I can make a big hole and pack
> lipids around the protein using INFLATEGRO script. But when I do the EM
> of the system the minimized system comes out at a very bad shape. I have
> also removed all the overlapping lipids but still EM doesn't run
> properly and gives me lots of LINCS warning. Also, my protein and lipid
> both are separately minimized.
>
> I am thinking of restraining the lipid in the Z direction and also
> restrain the full protein structure. But for CG i don't know what is the
> correct methodology to do this. Can anyone please let me know how to
> define the PR for the system consisting of CG lipids and CG protein and
> what specific commands to use for that?
>

If your system is so unstable that even EM fails, then applying restraints is
probably just delaying the inevitable crash.

If you feel you must apply PR (although I would strongly investigate the root
cause of your problem), position restraints for CG systems are just  
like for any
other system.  Use genrestr (with a suitable index file) to define a position
restraint .itp file for each of the species you wish to restrain.  Then simply
#include these files in the appropriate [moleculetype] directives in  
the topology.

-Justin