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]$
>>
>>
>> --
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Received on Sun Jul 27 2014 - 09:30:02 PDT
