[gmx-users] restraints on water oxygen atoms

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Jun 10 17:44:40 CEST 2013

Thanks for your reply.
When I look into the earlier gro file ( with APL even higher than 10% of desired APL), I still see some lipid residues in improper places, forexample in phenyl rings. How can I go on with it? If I choose the gro file without any overlap, the APL becomes very high and it would not be acceptable.
Do you still suggest not to delete lipids manually?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, June 10, 2013 4:50 PM
Subject: Re: [gmx-users] restraints on water oxygen atoms

On 6/10/13 3:37 AM, Shima Arasteh wrote:
> Thanks for your reply.
> The system I am trying to equilibrate is composed of popc/ peptide/ions/water. I built the system by InflateGRO methodology as you wrote in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, was used as the starting configuration in next steps. But before going on, I found some overlaps between lipids acyl chains and peptide structure. So tried to move the  lipid residues caused the overlaps. Then there are some gaps between peptide and near lipid chains. As a result, I see the water cleavage in these regions.
> Would you please give me any suggestions? How would I make a better packed system without disturbing overlaps or crashes?
> Would you please help me?

Don't manually delete lipids.  InflateGRO overestimates APL, so if you reach 
your target value, realize that the lipids are more packed than that and the 
true APL is much smaller.  I discuss that fact in the KALP-DPPC tutorial.  I 
generally stop packing when the lipids claim to be about 10% higher than the 
desired APL.  If you delete lipids because you've forced them together too much, 
then you're going to severely compromise the membrane.



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

gmx-users mailing list    gmx-users at gromacs.org
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list