I forgot to say this last time, but I think 1000 cycles is probably a little
too small... I would suggest sticking with the default (10 000) or maybe
going even a little higher (of course that depends on your system size...).
It may take a while to converge to the default gradient (more than 1000,
perhaps).
All the best,
Jason
On Thu, Jun 10, 2010 at 7:24 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Thu, Jun 10, 2010 at 10:51 AM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
>
>> I've been running gb, pb, and nmode analysis on an RNA/ligand system
>> using MMPBSA.py.MPI on two 8-core nodes (16 CPUs total).
>>
>> my input file is:
>>
>> &general
>> startframe=1, endframe=999999999, interval=1,
>> receptor_mask=':1-38', ligand_mask=':39', strip_mdcrd=0,
>> verbose=1, keep_files=1, entropy=1,
>> /
>> &gb
>> igb=1, gbsa=1, saltcon=0.200,
>> /
>> &pb
>> istrng=0.2, fillratio=4.0,
>> /
>> &nmode
>> nmode_igb=1, nmode_istrng=0.2, nminterval=200, maxcyc=1000,
>> /
>>
>> The gb and pb calculations are fine. Most of the nmode calculations are
>> okay.
>> But it looks like one of them won't finish. It reached the the maxcyc
>> number of
>> iterations and then increased maxcyc by a factor of 10. All the rest of
>> the
>> nmode tasks are finished except for this one and 10 hours later it is
>> still running.
>> I have had several jobs do this and they keep running indefinitely.
>>
>> First, why have a maxcyc if the program just increases it if it is
>> reached?
>>
>
>> Second, can you tell from the output what is going on with the
>> calculation? It
>> looks like the CG minimization is dying. Is it probably just a bad
>> structure that
>> won't minimize nicely? See out put at the bottom of this email.
>>
>
> I can't tell... I don't have much experience with xmin output through nab
> programs... The output is described on page 209 of the AmberTools 1.4
> manual.
>
>
>>
>> Third, how do I know which pdb was used for the calculations that produced
>> _MMPBSA_complex_nm.out.5? (I guess I could search through the code, but
>> I'll try asking here first.) Is it the sixth pdb produced by ptraj? In
>> my case
>> _MMPBSA_complex_nm.pdb.1001 ?
>>
>
> It depends. The suffix on the .out specifies which processor is creating
> the file, not specifically which frame it is. However, it is fairly simple
> to determine which frame corresponds to which processor. The number of
> frames is divided up equally amongst all processors. For n frames and m
> processors, each processor takes n/m frames. If n/m is not an integer, then
> for the number of remaining frames, that many processors (from rank 0 to
> remainder - 1) does 1 extra frame. This is all done in the order that ptraj
> writes out files. Moreover, processor 0 will take frames 0 - n/m (+1 if
> there are remainders).
>
>
>> Fourth, any suggestions for how to prevent the problem or at least
>> terminate the program when the problem occurs?
>>
>
> I will create a patch that does not increase the number of maxcyc if it's
> reached and send that to you soon. You can either kill the job if it's in a
> batch system or send it a termination signal (ctrl-C in unix, press it
> repeatedly to exit all processes).
>
> Hope this helps,
> Jason
>
>
>> Thanks for the help
>> --Niel
>>
>>
>> OUTPUT FROM _MMPBSA_complex_nm.out.5:
>>
>> Reading parm file (com.topo)
>> title:
>>
>> mm_options: ntpr=10000
>> mm_options: diel=C
>> mm_options: kappa=0.147010203727
>> mm_options: cut=1000
>> mm_options: gb=1
>> mm_options: dielc=4.0
>> mm_options: temp0=298.15
>> scaling charges by 0.500
>> iter Total bad vdW elect nonpolar genBorn
>> frms
>> ff: 0 -805.90 1966.92 -388.57 718.31 0.00 -3102.56
>> 1.99e+01
>> ________________________________________________________________
>> MIN: It= 0 E= -805.90 ( 19.856)
>> CG: It= 5 ( 0.413)q :-)
>> LS: i= 1 lhs_f= -759.27688 rhs_f= -0.15304093
>> lhs_g= 18.930947 rhs_g= 1377.3683
>> LS: step= 1 it= 1
>> MIN: It= 1 E= -1565.18 ( 5.645)
>> CG: It= 3 ( 0.473)q :-)
>> LS: i= 1 lhs_f= -99.283686 rhs_f= -0.019840063
>> lhs_g= 0.17934537 rhs_g= 178.56056
>> LS: step= 1 it= 1
>> ....
>> ....
>> ....
>> ....
>> MIN: It= 9702 E= -254.26 ( 0.013)
>> CG: It= 1 (999.999)q :-((
>> LS: i= 1 lhs_f= 0.0010889731 rhs_f= -8.8553167e-08
>> lhs_g= 0.0021649181 rhs_g= 0.0007969785
>> LS: i= 2 lhs_f= 3.2271245e-05 rhs_f= -1.4808629e-08
>> lhs_g= 0.00073717487 rhs_g= 0.0007969785
>> LS: i= 3 lhs_f= 1.2717392e-06 rhs_f= -2.5536537e-09
>> lhs_g= 0.00085998718 rhs_g= 0.0007969785
>> LS: i= 4 lhs_f= 1.1181794e-07 rhs_f= -5.1091314e-10
>> lhs_g= 0.00088042224 rhs_g= 0.0007969785
>> LS: i= 5 lhs_f= 1.7803018e-08 rhs_f= -1.0507513e-10
>> lhs_g= 0.00088448091 rhs_g= 0.0007969785
>> LS: i= 6 lhs_f= 4.0517989e-09 rhs_f= -2.1713693e-11
>> lhs_g= 0.00088531453 rhs_g= 0.0007969785
>> LS: i= 7 lhs_f= 1.4933903e-09 rhs_f= -4.4752754e-12
>> lhs_g= 0.00088548692 rhs_g= 0.0007969785
>> LS: i= 8 lhs_f= 9.0960839e-10 rhs_f= -9.0468856e-13
>> lhs_g= 0.00088552262 rhs_g= 0.0007969785
>> LS: i= 9 lhs_f= 7.8819085e-10 rhs_f= -1.6832494e-13
>> lhs_g= 0.00088552999 rhs_g= 0.0007969785
>> LS: i=10 lhs_f= 7.7579898e-10 rhs_f= -2.1976357e-14
>> lhs_g= 0.00088553145 rhs_g= 0.0007969785
>> LS: i=11 lhs_f= 7.8921403e-10 rhs_f= -8.4068087e-16
>> lhs_g= 0.00088553166 rhs_g= 0.0007969785
>> LS: i=12 lhs_f= 7.6067863e-10 rhs_f= -1.4793792e-18
>> lhs_g= 0.00088553167 rhs_g= 0.0007969785
>> LS: i=13 lhs_f= 7.5692697e-10 rhs_f= -4.7951204e-24
>> lhs_g= 0.00088553167 rhs_g= 0.0007969785
>> LS: i=14 lhs_f= 7.5692697e-10 rhs_f= -8.8553167e-28
>> lhs_g= 0.00088553167 rhs_g= 0.0007969785
>> LS: step= 1e-20 it=14
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 10 2010 - 17:30:04 PDT
