[gmx-users] Re: Need Help about GROMACS.

Justin A. Lemkul jalemkul at vt.edu
Mon May 17 16:25:31 CEST 2010

Regardless of whether or not you've received a response, please keep all 
correspondence on the gmx-users list.  I am not a private tutor.  To what post 
are you referring?  The list is fairly high-traffic, so if it's been a long time 
since you posted, don't continue to wait for a response.  Post a new question, 
expanding upon your previous problem with any new details.  You're more likely 
to get help if you demonstrate you are trying to help yourself.

You're applying opposing forces between your lipids and water?  That certainly 
sounds like a recipe for collapse.  Perhaps if you can describe (by posting to 
the list) what you're doing, what you're hoping to accomplish, and what your 
.mdp settings are, you might get some more useful advice.


Archana S Achalere wrote:
> Dear  Dr. Justin Lamkul,
>  I apologies that I am writing directly to you the query about my 
> simulation. As since long I have not got any response of my query posted 
> on gmx-users.
> I am simulating  lipid bilayer (DPPC + water)  where I give equal and 
> opposite force (along bilayer normal) on lipid and water molecules
> I face two problems:
> 1. If I remove center of mass motion of whole System then the simulation 
> box stars suppressing  along z direction (bilayer normal) and eventually 
> simulation terminates after few thousands of time steps.
> 2. If I give two groups DPPC and water for center of mass motion removal,
> then bilayer moves along z direction (bilayer normal).
> Could you please give me some direction how to resolve this.
> Thank you.
> Regards,
> -Archana
> Department of Chemical Engineering,
> Indian Institute of Science,
> Bangalore, India.


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


More information about the gromacs.org_gmx-users mailing list