[gmx-users] RE: Energy Minimization - not getting correct lipid area

[Erica Hicks]

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] [ml-node+s5086n4998239h28 at n6.nabble.com]
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.