Hi Marek,
As stated in the update.7 bugfix info, there have been some improvements to
the parameters to fit file format that result in old files being
incompatible. Re-generate this file using the SET_PARAMS runtype and it
should work again. Rest assured all versions of paramfit undergo thorough
testing for all typical use cases.
A tutorial on paramfit is being prepared and will be released very soon,
which will provide a full explanation of all job control options and more
importantly a discussion of how to evaluate the resulting parameters for
quality.
Hope this helps,
Robin
On Mon, Jul 28, 2014 at 1:51 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hi Robin,
>
> thanks for the complex info. I have also one more for you :))
>
> After successful applying of the patch 7, the paramfit
> was not able to read angle parameters from the file where
> all the parameters for fitting was previously saved (i.e. parameters.in).
>
> SOLUTION:
>
> In "file_io.c" in function "read_parameter_file_v2" (cca lines 201-206)
>
> change:
>
> }
> } while (strncmp(line, "#### ANGL", 9)!=0);
>
> // Read in the angles
> while (strncmp(line,"#",1)!=0) {
> fgets(line,127,fptr);
>
> TO
>
> }
> } while (strncmp(line, "#### ANGL", 9)!=0);
>
> // Read in the angles
> fgets(line,127,fptr);
> while (strncmp(line,"#",1)!=0) {
>
> i.e. the first fgets in the "// Read in the angles" while cycle
> has to be placed before while header (the same as in bond section)
> otherwise,
> the "// Read in the angles" cycle will be skipped because in "line"
> variable
> is "#### ANGLE KT THEQ ####" at the moment when the
> "strncmp(line,"#",1)!=0" condition is firstly checked in the "// Read in
> the angles" cycle and so this condition has on the very
> start of the angle part value FALSE.
>
> Anyway would be a good idea to test functionality of any updated part of
> the software before
> it is released :))
>
> Regarding SEARCH_SPACE I checked the genetic algorithm part and I started
> to have doubts
> that the given implementation could guarantee the final results within the
> SEARCH_SPACE relative range around the initial value. So thanks for the
> confirmation.
> Anyway something like your actual explanation should be placed in the
> Amber14 manual because
> the actual comments related to SEARCH_SPACE clearly suggest in my opinion,
> that the final
> values should be in SEARCH_SPACE relative distance from the initial values
> independently
> from the quality of the initial guesses.
>
> Thanks again,
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dne Mon, 28 Jul 2014 22:12:58 +0200 Robin Betz <rbetz.ucsd.edu> napsal/-a:
>
>
> Hi Marek,
>>
>> Thanks for your helpful bug report. I appreciate the time you took to look
>> at the code to figure out the source of each error. I've addressed each of
>> your bugs as follows:
>>
>> 1. Fixed in update.7.
>>
>> 2. Fixed in the development tree. A workaround is just to pass the -c and
>> -p parameters in the case of only one input topology.
>>
>> 3. There were two bugs causing the issue you saw. Both are now fixed in
>> the
>> development tree.
>>
>> First, if a job control file is passed to paramfit without any topology
>> files (the -i option only), the program will segfault for the reasons you
>> identified. This set of inputs doesn't make sense though, as if a job
>> control file is inputted there is no need for the wizard, but there is no
>> topology file to act upon. In this case paramfit will now output an error
>> about inconsistent command line options.
>>
>> Secondly, if a job control file and a parameter file are passed to
>> paramfit
>> (the -i and -p/-pf options), and the NSTRUCTURES=<number> line is present
>> in the job control file, the program will segfault. This is because the
>> number of structures is a property of the coordinate structure, which has
>> not been allocated due to the absence of the -c/-cf command line options.
>> Paramfit will now output an error if this scenario is present. This is
>> also
>> why it might have worked with your input files but not with the wizard
>> ones, as the NSTRUCTURES line is always present in the files that the
>> wizard writes.
>>
>> A workaround for this is to always pass a topology and coordinate file to
>> paramfit.
>>
>> 4. This is normal behavior. To clarify, the SEARCH_SPACE parameter only
>> affects the starting population of the genetic algorithm, and the final
>> parameters are free to be outside this range. The parameters in the
>> population can drift from the starting range by either the mutation
>> operation or the simplex refinement. If you're repeatedly seeing
>> convergence to other values there is most likely a very large difference
>> in
>> fitness between your starting search area and where the algorithm ends up.
>> You can encourage the algorithm to remain in certain areas of parameter
>> space by reducing the mutation rate (MUTATION_RATE=<0-1.0>) and removing
>> the simplex refinements altogether (GENERATIONS_TO_SIMPLEX=0).
>>
>> I will let you know when the next official patch is released.
>> Thanks again,
>>
>> Robin
>>
>>
>> On Sun, Jul 27, 2014 at 9:12 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>>
>> Hi Robin and all,
>>>
>>> I analyzed some of the actual paramfit problems (the most of all
>>> I mentioned before except the SEARCH_SPACE parameter problem).
>>> I am also suggesting some solutions for those who would like
>>> to use it before the proper patch will be released.
>>>
>>> Solved/analyzed problems:
>>>
>>> #1
>>> Ignoration of the K value if this should be read in from the "Job Control
>>> File" (JCF)
>>> or from the prmtop_list file.
>>>
>>> SOLUTION:
>>>
>>> in file "process_prmtop.c" , in line : 397 (func. process_single_prmtop)
>>> comment (//) or delete "parm_data->K=0.".
>>> There is too late for default setting of this parameter at this place.
>>>
>>> #2
>>> Paramfit crashes when one uses prmtop_list and mdcrd_list approach
>>> (i.e. paramfit -i Job_Control.in -pf prmtop_list -cf mdcrd_list -v MEDIUM
>>> --random-seed seed )
>>> in the case that there is just one prmtop/mdcrd file (just one molecule).
>>>
>>> This should not happen even if in such a case one may use recommended way
>>> for one molecule fit,
>>> without using prmtop_list and mdcrd_list.
>>> (i.e. paramfit -i Job_Control.in -p prmtop -c mdcrd -q QM_data.dat )
>>>
>>> SOLUTION:
>>>
>>> in file "read_mdcrd.c", in line : 35 (func. read_mdcrds)
>>> change "if (global_options->num_prmtops>1)" to "if
>>> (global_options->num_prmtops>=1)"
>>>
>>> #3
>>> Paramfit crashes when one strts it without any parameters i.e. in "wizard
>>> mode" in
>>> the moment when K value is read in.
>>>
>>> REASON
>>>
>>> That critical moment corresponds to the line : 181 (func.
>>> job_control_wizard) where
>>> is written command: "parm_datas[0].K=get_float();"
>>> Unfortunately the pointer "parm_datas" has at this moment value NULL or
>>> (nil) (depend on compiler)
>>> which probably means that at this moment this pointer still dos not
>>> represent any parm_struct structure (no proper memmory allocation was
>>> done
>>> yet using parm_datas pointer).
>>>
>>> In this context is strange to me that the same problem does not occure in
>>> case when JCF is already created by hand (not by wizard).
>>>
>>> I would assume that the command "parm_data[0].K=double_temp1;" (line :
>>> 366
>>> in process_job_control_setting.c) will also cause the program crash here
>>> because it seems, that the parm_datas is used for the allocation of the
>>> parm_struct structures array in function "read_prmtops" which is in the
>>> main function (in parameter_optimiser.c) called after the calls of
>>> "read_job_control_file" OR "job_control_wizard".
>>>
>>> #4
>>> Parameter SEARCH_SPACE does not seem to be fully functional (this problem
>>> I had also in the previous versions of paramfit). At least in the case of
>>> the force constants there is some problem, otherwise it should not be
>>> possible that I get for one my angle force constant the final value
>>> -5.2256 if the starting value was 58.2894 and the SEARCH_SPACE
>>> parameter
>>> was set to value 0.5.
>>>
>>> In such a case I would expected that the final value of this force
>>> constant will be in the range from
>>> 58.2894 - 0.5*58.2894 to 58.2894 + 0.5*58.2894. Clearly the actual final
>>> value -5.2256 does not belong to this interval. I verified that there is
>>> not a problem with reading SEARCH_SPACE parameter from the JCF as the
>>> right
>>> value is clearly written in the screen. Anyway I just to be sure rewrote
>>> this value in "defaults.c" but this did not helped so the problem is
>>> clearly in the implementation/usage of this parameter.
>>>
>>> This problem is actual for GENETIC but also for SIMPLEX calculation
>>> mode.
>>>
>>> All the above described problems are related to the actual version of
>>> Amber Tools which are
>>> patched up to the patch 6.
>>>
>>> Patch 7 from the 17 July, where also some paramfit problems were
>>> addressed
>>> was
>>> not applied because it was not possible. I describe this in the separate
>>> email.
>>> But anyway above described problems are probably not fixed in p.7 as
>>> Robin
>>> wrote (25 July) that they will be fixed in some next patch.
>>>
>>> Best wishes,
>>>
>>>
>>> Marek
>>>
>>>
>>>
>>>
>>>
>>>
>>> Dne Fri, 25 Jul 2014 17:33:37 +0200 Robin Betz <rbetz.ucsd.edu>
>>> napsal/-a:
>>>
>>> Hi Marek,
>>>
>>>>
>>>> This is a known bug with paramfit and will be fixed in the next few
>>>> days.
>>>> I
>>>> will let you know when the update is released.
>>>>
>>>> Regards,
>>>> Robin Betz
>>>> On Jul 24, 2014 3:05 PM, "Marek Maly" <marek.maly.ujep.cz> wrote:
>>>>
>>>> Dear all,
>>>>
>>>>>
>>>>> I just wanted to do some "revision" ff parameters fitting using the
>>>>> paramfit from the
>>>>> actual Amber14. When I tried to use this actual paramfit version for
>>>>> FIT
>>>>> work,
>>>>> I realized that the value of the constant K clearly written in the
>>>>> control
>>>>> file
>>>>> (K=-196.792733) was not read in and instead default value of K (i.e.
>>>>> 0.0000) is
>>>>> used and written in the screen.
>>>>> So I decided to use recommended wizard to create control file (however
>>>>> in
>>>>> case of
>>>>> the older paramfit versions I never had problem with control file
>>>>> created
>>>>> by hand).
>>>>>
>>>>> Unfortunately the wizard failed exactly in the step where it had to
>>>>> read
>>>>> K constant value,
>>>>> please see below. I verified this behavior on two different HW
>>>>> platforms.
>>>>>
>>>>> So it seems that the actual paramfit version (at least the my OpenMP
>>>>> version) has some problems
>>>>> in reading of the floating point numbers (from the file and as well
>>>>> from
>>>>> the screen (wizard)).
>>>>>
>>>>> I tried here to change the number of cores (using OMP_NUM_THREADS)
>>>>> from 8
>>>>> to 1 (for the wizard work) but this did not helped. I would be very
>>>>> grateful for any useful suggestions which could help me to
>>>>> solve this problem.
>>>>>
>>>>> I am using Amber14 with the patches up to 3 (in case of AT up to 6).
>>>>> My OS is CentOS release 6.5 (2.6.32-431.el6.x86_64), I used gnu
>>>>> compilers
>>>>> to compile Amber14 ( gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)
>>>>> ).
>>>>> I did not recognize any other problems (e.g. durin MD simulation) and
>>>>> all
>>>>> the
>>>>> tests which are recommended part of the Amber14 installation proceeded
>>>>> successfully.
>>>>>
>>>>> Thank you in advance for the help,
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> Marek
>>>>>
>>>>>
>>>>> ! Setting verbosity to medium.
>>>>>
>>>>>
>>>>> *****************************************************
>>>>> * AMBER Bond Angle and Dihedral Parameter Optimiser *
>>>>> * *
>>>>> * v3.0.0 *
>>>>> * *
>>>>> * Written by: *
>>>>> * Robin Betz (2011) *
>>>>> * Ross Walker (2004) *
>>>>> * The Walker Molecular Dynamics Lab *
>>>>> * University of California, San Diego *
>>>>> * La Jolla, California, 92092 *
>>>>> * USA *
>>>>> *****************************************************
>>>>>
>>>>>
>>>>> ************************************************************
>>>>> *************************
>>>>> Execution started at:
>>>>> | Thu Jul 24 23:31:16 2014
>>>>>
>>>>> |
>>>>> | Running OpenMP version of code using 1 processors
>>>>>
>>>>> | Random seed = 1406237476
>>>>> PARAMFIT SETTINGS WIZARD
>>>>> ------------------------
>>>>>
>>>>> Enter a job control filename to save settings as, or hit enter
>>>>> > control.in
>>>>> Saving job control settings as "control.in"
>>>>>
>>>>> How many input structures do you have?
>>>>> 100
>>>>>
>>>>> Which format is your coordinate file in?
>>>>> 1) Trajectory (.mdcrd,.inpcrd)
>>>>> 2) Restart (.rst, .restart)
>>>>> 1
>>>>>
>>>>> What type of job do you want to run?
>>>>> 1) Create input files for quantum program
>>>>> 2) Set which parameters to fit
>>>>> 3) Conduct a fit
>>>>> 3
>>>>>
>>>>> Which parameters would you like to fit?
>>>>> 1) Defaults (see manual)
>>>>> 2) Load list from file
>>>>> 3) K only
>>>>> > 2
>>>>> Enter file name:
>>>>> > parameters.in
>>>>> Enter the initial value for K:
>>>>> > -196.792733
>>>>> Error: signal 11:
>>>>> /opt/amber14/bin/paramfit[0x4090d5]
>>>>> /lib64/libc.so.6(+0x329a0)[0x7f83cdff79a0]
>>>>> /opt/amber14/bin/paramfit[0x421bf9]
>>>>> /opt/amber14/bin/paramfit[0x40a561]
>>>>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f83cdfe3d1d]
>>>>> /opt/amber14/bin/paramfit[0x401739]
>>>>> [mara.node25 04_FIT]$
>>>>>
>>>>>
>>>>> --
>>>>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>>>> http://www.opera.com/mail/
>>>>>
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Received on Mon Jul 28 2014 - 18:00:03 PDT
