On Thu, Aug 25, 2011, Sergey Samsonov wrote:
>
> I've been running steered MD with AMBER 10 and I'm facing a kind of
> weird problem. I use the same version of AMBER on 4 different
> architectures. On 3 of them everything works fine, on the last one the
> same input files yield very weird output in what is related to
> restraints part. Here are these parts of the outputs:
> 1. Normal run:
> R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 = 100.000 RK3 =
> 100.000
> R1A= -45.000 R2A= 55.000 R3A= 55.000 R4A= 155.000 RK2A= 100.000 RK3A=
> 100.000
> Rcurr: 14.989 Rcurr-(R2+R3)/2: 0.011 MIN(Rcurr-R2,Rcurr-R3): 0.011
>
> -----------------------
>
> 2. "Weird output":
>
> R1 = 115.000 R2 = 115.000 R3 = 115.000 R4 = 115.000 RK2 = 100.000 RK3 =
> 100.000
> R1A= -45.000 R2A= 55.000 R3A= 55.000 R4A= 155.000 RK2A= 100.000 RK3A=
> 100.000
> Rcurr: 14.989 Rcurr-(R2+R3)/2: 100.011 MIN(Rcurr-R2,Rcurr-R3): 100.011
>
> -----------------------
>
> Here is my restraints file, which is the same for both as well as input
> file is the same:
> ------------------------
> # Restraints for the centers of mass
> &rst iat=-1,-1, r2=15.00, rk2=100, r2a=55.00, ir6=0, igr1=1095 ,
> igr2=2115,2134,2144,2171,2177,2192,2213,2234,2241,2256,2270,2289,2301,2311,2330,2354,2366,2376,2395,2409,2416,
> &end
> In first case the given r2 in input is read correctly and r1, r3, r4 are
> calculated automatically.
> In the second case all r1, r2, r3 and r4 are wrongly assigned to the
> value, which is equal to the r2 in input +100.
The values of r1,r2,r3,r4 are "sticky" if you don't specify them explicitly,
they are not "calculated automatically"; rather, they take the values they had
in the previous rst namelist. If there is no previous rst namelist, you may
well get undefined behavior.
See if you can fix the problem by explicitly setting all the variables to the
values you want them to have.
...dac
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Received on Thu Aug 25 2011 - 07:30:04 PDT
