From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Tue Mar 02 2010 - 09:51:21 CST
ah, I was wondering if I should do that, thank you, but the dimensions listed in the xsc file are exactly the same as the ones I started with. But if I measure, in VMD, the dimensions of the .coor output file I am using as the starting coordinates for this run, the box dimensions are bigger than those listed in the xsc file. Is that OK?
From: $BNS_at_11+(B [linxingyu1986_at_gmail.com]
Sent: Monday, March 01, 2010 10:08 PM
To: Mark M Huntress
Subject: Re: namd-l: cell basis vector restart
read the box vector from the last xsc file when you restart your simualtion
On Tue, Mar 2, 2010 at 6:47 AM, Mark M Huntress <markmh_at_bgsu.edu<mailto:markmh_at_bgsu.edu>> wrote:
Hi, I just did a slow heat, for which I set my cell basis vectors equal to the solvent box dimensions. After the slow heat, the box has increased in size. Do I need to respecify the cell basis vectors to the larger values when restarting?
-- Xingyu Lin Currently: National Institute of Biological Sciences, Beijing Dr. Niu Huang's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206
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