On Thu, Aug 25, 2011 at 10:31 AM, Sergey Samsonov <
sergeys.biotec.tu-dresden.de> wrote:
> Thank you, David,
>
> 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'm also guessing different compilers (at least compiler versions) were used
in this case... It'll be easier to reproduce your issues if we can more
closely reproduce your system.
All the best,
Jason
> Best regards,
>
> Sergey
>
>
> 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.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Sergey A. Samsonov
> Postdoctoral researcher
> Structural Bioinformatics
> Biotechnology Center
> Tatzberg 47-51
> 01307 Dresden, Germany
>
> Tel: (+49) 351 463 400 83
> Fax: (+49) 351 463 402 87
> E-mail: sergey.samsonov.biotec.tu-dresden.de
> Webpage: www.biotec.tu-dresden.de
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 25 2011 - 09:30:02 PDT
