Hi Melissa,
Perhaps you missed Dave Case's response to your earlier copy of this email, that should have arrived overnight. Here it is again:
(quoted)
Odd. I'd first do non-parallel runs (for just a few steps) to see if the
problem is related to the parallel implementation. Also try pmemd to see if
what results that gives (again, just for a few steps).
I'm suspecting that you will have to post your files so that someone can try
to reproduce the problem.
....dac
On 9/05/2012, at 11:19 AM, Melissa Buskes wrote:
>
>
>
> Hello,
>
> I am currently attempting to run a minimisation of a complex (Inhibitor and protein) using Sander. I have been having problems running this on AMBER 11 with the following output files displaying this "error":
>
> | Local SIZE OF NONBOND LIST = 4301123
> | TOTAL SIZE OF NONBOND LIST = 16457817
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -Infinity NaN 1.7578E+06 O 1901
>
> BOND = 1086.8743 ANGLE = 2985.4907 DIHED = 3754.6339
> VDWAALS = 214218.6554 EEL = -113699.4160 HBOND = 0.0000
> 1-4 VDW = -Infinity 1-4 EEL = -Infinity RESTRAINT = 0.0000
>
> I then resubmitted the jobs on AMBER 10 and the jobs appeared to run fine. This is the same component of the output file:
>
> Local SIZE OF NONBOND LIST = 4299672
> | TOTAL SIZE OF NONBOND LIST = 16453545
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 9.1094E+05 5.2338E+04 1.1077E+07 HB3 1874
>
> BOND = 1086.8743 ANGLE = 2985.4907 DIHED = 3754.6340
> VDWAALS = 1000086.7124 EEL = -113709.9625 HBOND = 0.0000
> 1-4 VDW = 1382.9392 1-4 EEL = 15352.7435 RESTRAINT = 0.0000
>
> Is there maybe something that I have overlooked in regards to differences between AMBER 10 and 11? As I am using the exact same input files in both cases.
>
> Initially, I thought this result may have been an issue with clashing atoms, but I have since checked and resolved that these do not exist anymore.
>
> Any help/ suggestions would be much appreciated,
>
> Thank you,
>
> Melissa
>
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>
> ---------------------------------------------
> Melissa Buskes
> PhD student
> Department of Chemistry | School of Molecular Science
> La Trobe University
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Received on Tue May 08 2012 - 17:00:03 PDT
