On Thu, Aug 25, 2011, Sergey Samsonov wrote:
>
> now I put all the values for r1, r2, r3 and r4 explicitly as they are in
> the "correct" run, still all of them are assigned to be 115 (which is
> r2+100).
> So it is really puzzling, why it doesn't work properly. The only
> difference we have in different machines for AMBER is that in one case
> (when everything works) it is SUSE Linux, and in another case it is Red
> Hat.
I vaguely remember seeing a problem like this before, but I don't know how
to find it in the archives. Can you tell us what compilers you are using
on the machine that fails (output from "gcc -v" and "gfortran -v" if you are
using GNU compilers)? Also, which version of Red Hat is it? Is this a serial
run? Are there lots of restaints (and this is the only bad one), or is what
you show the only restraint?
Maybe someone else on the list has a better memory than I do. (OK, I *know*
lots of people have better memories in general -- maybe someone will recognize
this symptom.)
...dac
Original problem report below:
>
>
> On 08/25/2011 04:21 PM, David A Case wrote:
> > 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.
> >
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Received on Thu Aug 25 2011 - 08:30:06 PDT
