Hi, I went back and found that a possible error could be that the coordinate file was not updated correctly. After concatenated the Kalp_newbox.gro and dppc128_whole.gro, it said to update the coordinate file with the correct number of atoms. This should be the topology.top, right? But when I look through this, all I find is: [ molecules ] ; Compound #mols Protein 1 Where should the number of atoms be and is topology.top the correct file?
Erica ________________________________ From: Justin A. Lemkul [via GROMACS] [[email protected]] Sent: Friday, June 08, 2012 4:02 PM To: Hicks, Erica Subject: Re: Energy Minimization - not getting correct lipid area On 6/8/12 4:57 PM, Erica Hicks wrote: > It was after just one iteration. The number of lipids removed after scaling > the lipids by a factor of 4 was two. I am not sure how to update this as the > [molecules] directive in the topology.top shows only the number of moles, > i.e. 1. > The number shown in [molecules] is the number of molecules of a given species. If you started with 128 lipids, a removal of 4 means you need to list 124 lipids. I don't know how you can get such a small area with only one iteration of shrinking. Your box should be enormous at that point. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [hidden email]<UrlBlockedError.aspx> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [hidden email]<UrlBlockedError.aspx>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ________________________________ If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.n6.nabble.com/Energy-Minimization-not-getting-correct-lipid-area-tp4998235p4998239.html To unsubscribe from Energy Minimization - not getting correct lipid area, click here<http://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4998235&code=ZXJpY2EuaGlja3NAbXkudW5kLmVkdXw0OTk4MjM1fC0xMTYzMzMyODk1>. NAML<http://gromacs.5086.n6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> -- View this message in context: http://gromacs.5086.n6.nabble.com/Energy-Minimization-not-getting-correct-lipid-area-tp4998235p4998241.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
