Thanks !
Best,
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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>> http://www.opera.com/mail/
>>
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Received on Fri Jul 25 2014 - 09:30:02 PDT
