From: Jeffrey Potoff (jpotoff_at_wayne.edu)
Date: Thu Mar 18 2021 - 17:27:10 CDT
If you know the area per lipid for the lipid of interest, couldn’t you calculate the surface area of your sphere and divide by the area per lipid to get the (approximate) number of lipids required?
--- Jeffrey Potoff Interim Chair, Department of Chemical Engineering and Materials Science College of Engineering Wayne State University From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> On Behalf Of Ropon-Palacios G. Sent: Thursday, March 18, 2021 6:19 PM To: Mike McCallum <mmccallum_at_PACIFIC.EDU>; KS UIUC <namd-l_at_ks.uiuc.edu> Subject: Re: namd-l: Lipid into sphere [EXTERNAL] Yes, but I want calculate number of lipid to placed given an radius of sphere in my case is 425 angstrom From: Mike McCallum <mmccallum_at_PACIFIC.EDU<mailto:mmccallum_at_PACIFIC.EDU>> Date: Thursday, March 18, 2021 at 5:13 PM To: KS UIUC <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>, "Ropon-Palacios G." <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>> Subject: Re: namd-l: Lipid into sphere Hi Geo., I’d look into PACKMOL. It should be able to do exactly this for you, and it is easy to use. https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml__;!!DZ3fjg!r6lC50g0XjgTZFN17r7ozq7ybNmR9XiXYuKs_ZyNtI7N-vB9liFsYeGYs4HT4YWRQw$ <https://urldefense.com/v3/__http:/leandro.iqm.unicamp.br/m3g/packmol/home.shtml__;!!DZ3fjg!tEJyvrvToC26sOR6PHbYrgfoYR45N1eLtftgToUwnflxGDY0Qrw8HU6arViDo6iSjg$> Best Mike On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. <biodano.geo_at_gmail.com<mailto:biodano.geo_at_gmail.com>> wrote: Dear NAMD users, How can calculate lipid (POPE) number to be placed into an sphere the 425 Angstrom. Best, Geo. -- C. Michael McCallum Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax
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