[gmx-users] Re: Need Help about GROMACS.
Justin A. Lemkul
jalemkul at vt.edu
Tue May 18 14:44:12 CEST 2010
Archana S Achalere wrote:
> Thank you Dr. Justin for the reply.
> Here are the details of my simulation.
> I am simulating lipid bilayer (DPPC + water) where I give equal and
> opposite force (along bilayer normal) on lipid and water molecules
> I am using 128 DPPC and 3655 water. The .pdb file is taken from
> Prof. Tieleman's page, University of Calgary.
> I am trying to calculate water flux across the bilayer.
> I apply the force by using nonequilibrium MD simulation option in .mdp
> file, where the acceleration on two groups DPPC and water is given such
> that the total force on each group would be equal and opposite.
> I face two problems:
> 1. If I remove center of mass motion of whole System then the simulation
> box starts suppressing along z direction (bilayer normal) and eventually
> simulation terminates after few thousands of time steps.
Well, you face a tenuous position. You are forcing two groups together, and
unless they are delicately balanced, you'll wind up just crashing the whole
> 2. If I give two groups DPPC and water for center of mass motion removal,
> then bilayer moves along z direction (bilayer normal).
I would think that this is the correct method for COM motion removal, but what
you're seeing suggests there is a net force on the system (see below).
> ; Non-equilibrium MD stuff
> acc-grps = DPPC SOL
> accelerate = 0.0 0.0 0.07 0.0 0.0 -0.1
Using these accelerations, you have a slight imbalance in your forces. Using
some crude and quick calculations:
DPPC = 734 amu, water = 18 amu
734*128 = 90282
18*3655 = 65790
90282*0.07 = 6319.74
65790*0.1 = 6579
The two resulting forces should be equal in magnitude, but as you can see, they
are not. The force applied by the water exceeds that applied by DPPC, so you
see the net motion along the z-axis.
> freezegrps =
> freezedim =
> cos-acceleration = 0
> deform =
> On Mon, 17 May 2010, Justin A. Lemkul wrote:
>> 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
>>> then bilayer moves along z direction (bilayer normal).
>>> Could you please give me some direction how to resolve this.
>>> Thank you.
>>> Department of Chemical Engineering,
>>> Indian Institute of Science,
>>> Bangalore, India.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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