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 - 13:25:14 CDT

What is the chip? The compiler? The config file? This is definitely a
config or compiler or unsupported s/w or h/w problem. - Bob Duke
----- 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
>>
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