Re: Inquiry about lipid membrane simulation

From: Kenno Vanommeslaeghe (
Date: Wed Jun 18 2014 - 14:02:52 CDT

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?
- 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?
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).

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:53 CST