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

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 9 17:06:27 CET 2010

On 1/9/10 10:49 AM, chris.neale at utoronto.ca wrote:
> 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.

Are you sure that recent Gromacs versions still do this?  I requested a fix (for 
final output configurations only) with the original version 4.0, which I thought 
(if memory serves) was fixed as of version 4.0.2, released over a year ago.  Is 
this not the case?  I get intact output structures from everything I've done 
since 4.0.2.

Trajectories certainly still contain "broken" frames, the confout.gro should not 
be an issue.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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