Dropping significantly is normal. I suggest printing every step, to see
what happens right at the end.
One of my favorite hacks for all situations is to run a little md at 10K
instead of minimization, then minimize if you must. If your coordinates
are the problem, it might bump you out of the situation. I say this
since min ran a bit, indicating no basic problem with the model, so the
coordinates are suspect.
Bill
On 5/22/17 1:19 AM, Nikita Devnarain wrote:
> I've noticed that the energy dropped significantly just before the job
> terminated:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.3342E+05 1.7748E+00 1.7075E+02 H9 4147
>
> BOND = 10243.4116 ANGLE = 382.3810 DIHED =
> 4034.4069
> VDWAALS = 25801.7886 EEL = -184077.5659 HBOND =
> 0.0000
> 1-4 VDW = 1142.8143 1-4 EEL = 9051.0550 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -1.3425E+05 1.0214E+00 1.1301E+02 CD 2347
>
> BOND = 10299.3244 ANGLE = 442.4051 DIHED =
> 4033.8846
> VDWAALS = 25552.8101 EEL = -184186.6705 HBOND =
> 0.0000
> 1-4 VDW = 950.9742 1-4 EEL = 8652.4050 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -3.1431E+05 1.1784E+06 1.8708E+08 H7 4100
>
> BOND = 10489.7320 ANGLE = 828.3905 DIHED =
> 4105.2686
> VDWAALS = 25580.9181 EEL = -184472.5186 HBOND =
> 0.0000
> 1-4 VDW = 778.4510 1-4 EEL = -171621.9397 RESTRAINT =
> 0.0000
>
>
> On Mon, May 22, 2017 at 10:12 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Noting that the stack indicates nonbonded adjustment as part of ewald
>> force calculation (likely as not), have you looked for any warnings or
>> odd energies in your output file prior to this event?
>>
>> Bill
>>
>>
>> On 5/22/17 12:54 AM, Nikita Devnarain wrote:
>>> Dear AMBER users
>>>
>>> I'm trying to minimise a complex with a receptor and 2 ligands, however,
>> I
>>> keep encountering the following error causing termination of the job:
>>>
>>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>>> reference.
>>>
>>> Backtrace for this error:
>>> #0 0x2AAAAC453BF7
>>> #1 0x2AAAAC452DF0
>>> #2 0x2AAAAD10124F
>>> #3 0x56C339 in nb_adjust_
>>> #4 0x56E268 in ewald_force_
>>> #5 0x7AAF93 in force_
>>> #6 0x4E3712 in sander_
>>> #7 0x4D93A6 in MAIN__ at multisander.F90:?
>>>
>>>
>>> Could anyone assist me with what has been causing this?
>>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon May 22 2017 - 01:30:04 PDT
