AMBER Archive (2009)

Subject: Re: [AMBER] Error with calculation of the potential energy

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Apr 27 2009 - 13:46:43 CDT


Also, note that there is no legitimate way the delr is actually 0, and this
is an known test with a good configuration (dhfr). SO there is something
way more fouled up than needing to disable floating point exceptions. At
least in the past I have not disabled exceptions I believe unless it was the
compiler default; I think new config options for ifort include -fast, which
may actually disable exceptions (I finally gave in to the general trend on
this and have not taken time to review the decision).
Regards - Bob
----- Original Message -----
From: "Per Jr. Greisen" <pgreisen_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Monday, April 27, 2009 1:11 PM
Subject: Re: [AMBER] Error with calculation of the potential energy

Hi,

When I try to test the pmemd it seems that it has an error with
calculating the potential energy - I put out the output from some of
the tests.

export TESTsander='../../exe/pmemd'; cd dhfr && ./Run.dhfr

which returns some of the following in the TEST_FAILURES.diff

78,79c78,79
< NSTEP = 1 TIME(PS) = 510.051 TEMP(K) = 301.29 PRESS =
0.
< Etot = -57751.8286 EKtot = 14110.5335 EPtot =
-71862.3622

---
>  NSTEP =        1   TIME(PS) =     510.051  TEMP(K) =   301.65  PRESS = 
> 0.
>  Etot   =      3706.9950  EKtot   =     14127.5125  EPtot 
>   =    -10420.5175
81,82c81,82
<  1-4 NB =       545.9440  1-4 EEL =      6666.3920  VDWAALS    =
 8109.3892
<  EELEC  =    -89881.6441  EHBOND  =         0.  RESTRAINT  =         0.
---
>  1-4 NB =       545.9440  1-4 EEL =      6666.3920  VDWAALS 
>      -727.9808
>  EELEC  =    -19602.4294  EHBOND  =         0.  RESTRAINT  =         0.
84,88c84,88

so it seems that it has not been compiled correctly; here it is compiled with ftrap=%none - if I on the other hand compile remove that compiling option the pmemd ends with FPE - division by zero. If I write the following part out in pairs_calc_vec.i by modifying the code:

! Do the Coulomb part of the direct sum using erfc spline table:

delr = sqrt(delr2) write (0,*) delr

delr is set to zero - how to fix this and why should one compile with ftrap=%none?

Thanks in advance

Best regards

Per

On Mon, Apr 27, 2009 at 1:08 PM, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote: > please give more info- you said serial, parallel and pmemd, but only give > 2 > examples so we don't know where to look for the problem. also give the > whole > section from the energy, not just the totals, so we can see which > components > differ. finally, did all of the test cases pass? > > On Mon, Apr 27, 2009 at 7:03 AM, Per Jr. Greisen <pgreisen_at_gmail.com> > wrote: > >> Hi all, >> >> I have compiled a serial, parallel, and pmemd of amber but I get some >> strange results when I try to run the test examples it seems that the >> potential energy is calculated wrongly in the different test cases >> >> < NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.21 >> PRESS = -5.8 >> < Etot = -608.3990 EKtot = 1063.0604 EPtot = >> -1671.4594 >> --- >> > NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.03 PRESS = >> -961.1 >> > Etot = 1257.0312 EKtot = 1062.3997 EPtot = >> 194.6315 >> 93,95c93,95 >> >> Any suggestions on how to fix this? Thanks in advance >> >> With kind regards >> >> Per >> >> _______________________________________________ >> AMBER mailing list >> AMBER_at_ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER_at_ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber >

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