Re: [AMBER] irest

From: Cenk \(Jenk\) Andac <"Cenk>
Date: Wed, 9 Mar 2011 07:07:05 -0800 (PST)

Hi Burcu,
You may want to try to manually edit your restart file (the coordinate file formed with the -r flag in your MD run) as follows.
MOL                                  (Line 1)                              
*4568**0.1020000E+04        (Line 2)
17.5484816 2.0554241 22.0876858 18.2851020 3.2335462 22.1281610
18.9663293 3.7550160 21.0214884 18.8204758 2.9840031 19.8848481
18.1222181 1.8053273 19.7994809 17.4522890 1.3629498 20.8915859
16.8065876 0.1170148 20.8447177 17.9902558 1.1593978 18.6079914

You need to add the velocity information in line 2 of your restart file. I placed the stars (*) to indicate the number of spaces (you need to replace those stars with spaces). There  4568 is the total number of atoms in your system including water, ions etc.  and  0.1020000E+04  corresponds to 1020 picoseconds, the final time indicated in your MD energy output file.
you may restart your md run by adding 'irest=1, ntx=5'  in your md input file. 
Hope this works out ok for you.

Cenk Andac, M.S., Ph.D.
Currently appointed as a post doc researcher in the School of Pharmacy
at Ankara University, Ankara TR. 

Department of Pharmacology
Medical School at
Dicle University-Diyarbakir TR
M.S., School of Pharmacy at
the University of Wisconsin-Madison WI USA
Ph.D., School of Pharmacy at
Gazi University-Ankara TR
Cell: +90-(536)-4813012

--- On Wed, 3/9/11, Burcu Aykac Fas <> wrote:

From: Burcu Aykac Fas <>
Subject: [AMBER] irest
Date: Wednesday, March 9, 2011, 8:38 AM

Dear Amber users,

I would like to ask if anyone forgot to include irest and ntx parameters in
their *in files. I've forgotten them for two different 70 ns simulations and
I thought I've used my restart files. Probably the trajectories are useless
and I have to repeat my simulations!

Thank you,
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Received on Wed Mar 09 2011 - 07:30:05 PST
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