AMBER Archive (2006)

Subject: RE：AMBER: the problem of mdcrd

From: xiphias xie (xiphiasxp_at_yahoo.com.cn)
Date: Wed Jan 18 2006 - 02:54:18 CST

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
know
 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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