[gmx-users] restraints on water oxygen atoms

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Jun 10 18:24:37 CEST 2013

Would you please tell me which initial deletion radius?

And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, June 10, 2013 8:22 PM
Subject: Re: [gmx-users] restraints on water oxygen atoms

On 6/10/13 11:44 AM, Shima Arasteh wrote:
> 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?

I don't see how that's possible, quite honestly.  If the initial deletion radius 
was sufficient, then lipid molecules shouldn't force their way through phenyl 
rings - the forces required would be astronomical.

I don't have any details of your protocol, so it's hard to comment further.  If 
things are getting jammed together this badly, you should probably be shrinking 
more slowly than you currently are.

I never advocate for manual deletion of lipids, because, as you can see from 
experience, doing so creates a world of problems during equilibration.



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


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