Re: Inquiry about lipid membrane simulation

From: Mo Chen (
Date: Wed Jun 18 2014 - 14:25:16 CDT

Hi Kenno,

I am sorry I should have emailed to the NAMD list earlier. My answers to
your question is as below.

On Wed, Jun 18, 2014 at 12:02 PM, Kenno Vanommeslaeghe <> wrote:

> As a matter of policy, I do not answer this kind of questions per personal
> e-mail (nor do I debug people's input files in their stead). Additionally,
> I don't even know the answers to most of your questions; other people on
> this list do. The only thing I can offer is more questions:
> - does the membrane shrinkage also happen when you start your NAMD
> simulation from a CHARMM equilibrated structure?
> - what lipid(s) does your membrane consist of, and at what temperature are
> you simulating it?

The two sets of simulation were started from the same system. That is, I
used CHARMM to do equilibration and production, and parallelly I used NAMD
to do equilibration and production. I did not use the equilibrated
structure of CHARMM for NAMD production run, but I will definitely try that.

> - You seem to be using CHARMM-GUI (which you should have mentioned when
> first asking your question). CHARMM-GUI generates NAMD input files to allow
> its users to run production with NAMD. Is that what you're doing, or are
> you modifying the protocol? And in the latter case, why?

I started with CHARMM-GUI, and made some changes mostly in setting up the
systems, as I built the force field of a new molecule that is not available
in the CHARMM force fields. I did not make much changes in the
equilibration and production run files of CHARMM or NAMD from CHARMM-GUI,
except that I added some constraints on dihedral angles of the new

Comparing the CHARMM and NAMD equilibration and production input files from
CHARMM-GUI, I found that (1) NAMD input did not contain the lines to keep
water out from the lipid hydrophobic core in the Equilibration part, while
CHARMM input did; (2) CHARMM input uses a small potential of MMFP GEO
Cylinder ... for the solute, while NAMD did not. So I wonder if the
shrinking result came from these differences.

Thank you very much.


> Please answer these on the NAMD list; the information will help other
> members in trying to find the cause of your problem.
> On 06/18/2014 02:41 PM, Mo Chen wrote:
>> Hi Kenno,
>> Thank you very much for your prompt response.
>> I was only doing regular MD simulations, nothing special. I did the
>> simulation both in CHARMM and NAMD for a short term (10ns), and found that
>> CHARMM kept the unit cell dimension while NAMD did not, and the NAMD
>> trajectory showed that it converged to a much smaller area/lipid than the
>> standard value proposed in the CHARMM36 force field. Therefore, I figured
>> that maybe my NAMD configuration files were not correct (attached). As I
>> compared the inputfiles of CHARMM and NAMD, I found that NAMD input file
>> lacked the MMFP GEO Plane for water during equilibration stage and MMFP
>> GEO cylindrical for partially inserted protein segment during production
>> run to avoid protein drafting.
>> May I ask if any molecule should be constrained during production runs?
>> Thank you very much.
>> Best,
>> Mo
>> On Wed, Jun 18, 2014 at 8:20 AM, Kenno Vanommeslaeghe
>> < <>> wrote:
>> On 06/17/2014 09:57 PM, Mo Chen wrote:
>> 1) In CHARMM, the MMFP GEO PLANE ... is used to keep the
>> non-crystal water
>> molecules away from entering the hydrophobic core of lipid bilayer
>> I don't know what kind of study you're doing, but generally spoken,
>> that shouldn't be necessary, and is likely harmful. If, OTOH, the
>> function of the MMFP restraint is to keep the membrane aligned with
>> the box, then something can be said in favor of it (though I still
>> would do it differently).

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