[gmx-users] InflateGro methodology
shima_arasteh2001 at yahoo.com
Sun Sep 23 09:41:48 CEST 2012
I don't know! :))
----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, September 23, 2012 10:52 AM
Subject: Re: [gmx-users] InflateGro methodology
Why don't you just try it and see what happens?
On 2012-09-23 12:19:20AM -0700, Shima Arasteh wrote:
> Dear users,
> I wanna pack the lipids around my protein. To do so, InflateGro methodology is applied. Following Justin's tutorial KALP15-DPPC, the first step is scaling up 4 times:
> # perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat
> and then shrinking it for 26 times.
> I'd like to know if it is possible to scale up 6 times or more and then scale it down for around 30 times? Because when I scale up 4 times, I see 2,3 lipid chains are still in contact with the protein (I am not sure if this would be a major problem or not!) .
> Would you please advise me?
> Thanks in advance.
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Peter C. Lai | University of Alabama-Birmingham
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