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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>
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Received on Fri Jul 25 2014 - 09:00:02 PDT
