AMBER Archive (2007)Subject: Re: AMBER: Potential of mean force, how to calculate rate of dissociation?
From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Mon May 07 2007 - 07:26:55 CDT
wang wrote:
> Dear all ,
> When I used the SMD module , the moving distance is bigger than 100 A
> and the error happened .
> Could you tell me how to fix the problem ?
> thanks
>
> wang
>
>
> input
> ___________________________________________________
> &rst iat=1771,3787, r2=63., rk2 = 1000., r2a=300, /
> ____________________________________________________
>
>
> error message
> ____________________________________________________
>
> ******
> CA ( 1771)-CA ( 3787) NSTEP1= 0 NSTEP2=200000
> R1 = -37.000 R2 = 63.000 R3 = 63.000 R4 = 163.000 RK2 =1000.000 RK3 =
> 1000.000
> R1A= -37.000 R2A= 300.000 R3A= 300.000 R4A= 163.000 RK2A= 0.000 RK3A= 0.000
> Rcurr: 63.108 Rcurr-(R2+R3)/2: 0.108 MIN(Rcurr-R2,Rcurr-R3): 0.108
> ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
> Offending re
> straint:
> ******
> CA ( 1771)-CA ( 3787) NSTEP1= 0 NSTEP2=200000
> R1 = -37.000 R2 = 63.000 R3 = 63.000 R4 = 163.000 RK2 =1000.000 RK3 =
> 1000.000
> R1A= -37.000 R2A= 300.000 R3A= 300.000 R4A= 163.000 RK2A= 0.000 RK3A= 0.00
>
Dear Wang,
Did you apply all the bugfixes to amber? This sounds a lot like the bug
described in Bugfix.32. Take a look at:
http://amber.scripps.edu/bugfixes90.html
Gustavo.
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