AMBER: Re: RE:AMBER: the problem of mdcrd

From: Vlad Cojocaru <>
Date: Wed, 18 Jan 2006 10:48:36 +0100

The center command centers and does not image ... For imaging you have
the image command ..

Ok, now its clear what you do with the Temp ... it looks OK ... Probably
your system blows up at some point as Ross said... If you followed all
Ross's points and still didnt solve the issue, maybe you should play a
bit with the strength of the T bath (in case you are using T coupling --
see the TAUTP and &wt cards in the amber manual) ... I dont reemember
your script 100% but if you are using SHAKE (ntc=2) and a dt=0.002 you
might also experience problems at high temperature may consider
decreasing dt to 0.001...

This is what comes to my mind ... You should check carefully your output
... maybe outputing more frequently can help with solving your problem
... For instance what is the T profile during your runs??

Good Luck

xiphias xie wrote:

>Thank you very much !
>>for centering in ptraj see the center command in
>>ptraj (amber manual pp 200)
>Can the center command recenter my inpcrd file ? I
> it can reimaging the trajectory back into the primary
>box. but it seems no effect to my mdcrd files.
>>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 ..
>In the step 1 MD ,I raised the temperature from 0 K to
>356.65 K
>tempi = 0.0,
>temp0 = 356.65,.
>In the step 2 MD , I reduced the temperature from
>356.65 K to 300K .
>tempi = 356.65, temp0 = 300.0,
>I am not sure it is right .
>thanks very much !
> xiphias
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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 Thu Jan 19 2006 - 06:10:05 PST
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