From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Tue Jan 14 2014 - 02:19:55 CST
On 14 January 2014 06:34, Jeffrey Potoff <jpotoffx_at_gmail.com> 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 (dx.doi.org/10.1021/jp3059992 | 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
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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