AMBER: Re: REAMBER: the problem of mdcrd

From: Vlad Cojocaru <>
Date: Tue, 17 Jan 2006 13:40:41 +0100

for centering in ptraj see the center command in ptraj (amber manual pp 200)

regarding the temperature ... if you say that the reaction temp is 356,
I assume that should be temp0 and not tempi (unless you have a previous
run at high temp and you would like to decrease the temp to 300) . ...
If you want to do MD at 356, you should first equilibrate your system at
300 (starting first heating step with a tempi of 0 - or 10 is you wish,
depending on which T control you apply - see amber tutorials for
details) and only after your system was equilibrated at 300 you should
proceed with raising the temp to 356 ... From your previous email it is
not exactly clear what you are actually doing ..


xiphias xie wrote:

>>1) You initial coordinates are a long way from the
>>the origin. Create a pdb
>>file from the inpcrd file and see what you get for
>>the typical coordinate
>>range. If your initial system is a close to
>>exceeding the limit then try
>>using ptraj to recenter this coordinates and create
>>a new inpcrd file.
>How can i use ptraj to recenter coordinates ?
>like this ?
>trajin *.inpcrd
>trajout *.inpcrd
>thanks in advance!
>The AMBER Mail Reflector
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
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Received on Wed Jan 18 2006 - 06:10:07 PST
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