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

Archana S Achalere archana at chemeng.iisc.ernet.in
Tue May 18 17:54:27 CEST 2010

```I think the force I have applied on the two systems balance each other.
If I calculate total force on each group:

DPPC = 734 amu, water = 18 amu

734*128 = 93952 (This thing you calculated as 90282)
18*3655 = 65790

93952*0.07 = 6576.64
65790*0.1  = 6579

If I reduce values of acceleration   by one order of magnitude:

; Non-equilibrium MD stuff
acc-grps                 = DPPC SOL
accelerate               = 0.0 0.0 0.007 0.0 0.0 -0.01

and remove the center of mass motion of DPPC and water
the simulation works well. In this case bilayer do not move along Z
direction. But very few water can cross. So I am interested to give
higher force so that I can observe large amount of water crossing the
bilayer. Which I do see but then bilayer keeps moving along bilayer
normal.

-archana.

On Tue, 18 May 2010, gmx-users-request at gromacs.org wrote:

>
> Message: 1
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Need Help about GROMACS.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BF28B9C.9040206 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 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
> thing anyway.
>
>> 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).
>
> <snip>
>
>> ; 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.
>
> -Justin
>
>> freezegrps               =
>> freezedim                =
>> cos-acceleration         = 0
>> deform                   =
>>
>>
>>
>> -Regards,
>> Archana.
>>
>>
>>
>>
>>
>>
>>
>> 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
>>>
>>> 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
>>>
>>> -Justin
>>>
>>> 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.
>>>>
>>>
>>>
>>
>
>

--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

```