Re: MD simulation Patch grid errors

From: Thomas Evangelidis (
Date: Tue Jan 14 2014 - 02:19:55 CST

On 14 January 2014 06:34, Jeffrey Potoff <> wrote:

> On 1/13/2014 10:37 PM, Jiann George Pazhamalil wrote:
>> Hi,
>> Thank you for your responses,
>> The POPC membrane was made through charmmgui and then converted
>> accordingly to work in the lipid11 amber force field. I am attempting to
>> reduce the number of steps in the NAMD simulation and seeing if that would
>> alter the patch grid problem. From the logout files it is visible that the
>> system is shrinking at a high rate.
>> I thought this could be due to the surfacetenstiontarget parameter as
>> there are discrepancies between the units used in amber and namd. In the
>> lipid11 Amber the units were dyn/Angstrom (the value I found and am using)
>> and namd specifies it as dyn/cm but converting 17 to 17000000 doesn't seem
>> right. From the other mailing lists everyone seems to use a value closer to
>> 20. Is this parameter applying pressure from outside or from within the
>> system?
>> No, that is not correct. If you check the figure caption of Figure 4 in
> the Lipid 11 paper ( | J. Phys. Chem. B 2012,
> 116, 11124-11136), the units are listed as dyn/cm.
> "Figure 4. Area per lipid versus simulation time for lipid bilayer. All
> surface tension values are reported as dyn/cm per layer (abbreviated "dyn"
> in the legends)."
That's true. I simulated a POPE membrane patch with lipid11 in NAMD using
the suggested value (26 dyn) and I could reproduce the surface area and
electron density plots in the paper. You must use "SurfaceTensionTarget
17" instead.

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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