[gmx-users] request for future tools
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 29 10:25:41 CET 2005
Mark Abraham wrote:
> David Mobley wrote:
>
>> Dear all, (especially developers),
>>
>> I just wanted to put in a request for future development of g_energy
>> and similar tools:
Guys,
I have long been struggling with the same problem but was too lazy to
fix it. In my eyes the easiest solution would be to enter a string, e.g.
potential
or
temperature
and have g_energy looking for the energy that best matches it. This is
not complicated, and there really is no excuse for me not implementing
it. It could also be a command line option, e.g. g_energy -term
"potential kinetic total"
The only drawback is that the terms should not have spaces in the name
like Coulomb (SR) and Coulomb (LR), but even that can be fixed.
I'll try to do it before 3.3.1
>>
>> For scripting purposes, it would be really useful if the output
>> categories were not dependent on the details of the run. For example,
>> if I run g_energy on one of my free energy calculations with
>> orientational and distance restraints, the potential enery is #15 and
>> the dV/dlambda is #20. But without my orientational and distance
>> restraints, the potential energy is #10 and the dV/dlambda is #15. It
>> would be much better if both cases could be consistent and, in the
>> case without orientational restraints, the values corresponding to
>> restraint energies would simply return zero.
>
>
> I agree that it would be a good feature. It is "only" a matter of
> establishing a mapping of all possible output terms to an integer. This
> isn't easy if you have multiple (nonstandard) groups, because the
> interaction energies of the groups is reported in the .edr file and the
> number and identity of the groups isn't known at compile time. That can
> be gotten around by having their indices all greater than the largest
> index of a term known at compile time, or all letters, etc.
>
>> At present, it's really obnoxious from the perspective of writing
>> analysis scripts, as my analysis scripts either need to know whether
>> distance restraints are turned on or not (in order to extract the
>> correct energies, if I want, say, the potential energy) or they need
>> to somehow run g_energy, look for the potential, and figure out what
>> value to input to get it. Does anyone have an easier option?
>
>
> I don't know whether you would agree that the solution I suggest below
> is "easier", but it certainly works. I use the tool expect (found on all
> modern *NIXES) to do more advanced versions of the oft-recommended
>
> echo "3 0" | g_energy -f output.edr
>
> schemes, so that I can deal with a limited number of known .edr formats.
> Every time the script breaks you can add in a new format following the
> example below and use to your heart's content. The example below is an
> old attempt at extracting the total Coulomb energy from a gromacs 3.2.1
> .edr file that could have been calculated with various electrostatic
> methods. You could modify this suitably to treat your known range
> variation (email me if you want the file as an attachment). In theory an
> expect script could digest the g_energy output and synthesize the
> responses, but that would be overkill.
>
> Regards,
>
> Mark
>
> -----------------
>
> #!/usr/bin/expect -f
>
> # Usage: expect this_script.tcl command_to_automate [args]
>
> set force_conservative 0 ;# set to 1 to force conservative mode even if
> ;# script wasn't run conservatively originally
> if {$force_conservative} {
> set send_slow {1 .1}
> proc send {ignore arg} {
> sleep .1
> exp_send -s -- $arg
> }
> }
>
> set timeout -1
>
> # now construct and run the sub-process
> set cmd [list spawn ]
> foreach a $argv {
> lappend cmd $a
> }
> eval $cmd
>
> match_max 100000
> while 1 {
> expect {
> "End your selection with 0\r
> 1= Angle 2= Proper Dih. 3=Ryckaert-Bell. 4= LJ-14\r
> 5= Coulomb-14 6= LJ (SR) 7= Coulomb (SR) 8= Coul.
> recip.\r
> 9= Potential 10= Kinetic En. 11= Total Energy 12=
> Temperature\r
> 13=Pressure (bar) 14= Vir-XX 15= Vir-XY 16= Vir-XZ\r
> 17= Vir-YX 18= Vir-YY 19= Vir-YZ 20= Vir-ZX\r
> 21= Vir-ZY 22= Vir-ZZ 23= Pres-XX (bar) 24= Pres-XY
> (bar)\r
> 25= Pres-XZ (bar) 26= Pres-YX (bar) 27= Pres-YY (bar) 28= Pres-YZ
> (bar)\r
> 29= Pres-ZX (bar) 30= Pres-ZY (bar) 31= Pres-ZZ (bar) 32=
> #Surf*SurfTen\r
> 33= Mu-X 34= Mu-Y 35= Mu-Z 36= T-Protein\r
> 37= Lamb-Protein\r" { send -- "5 7 8 0\r" }
> "End your selection with 0\r
> 1= Angle 2= Proper Dih. 3=Ryckaert-Bell. 4= LJ-14\r
> 5= Coulomb-14 6= LJ (SR) 7= Coulomb (SR) 8= Potential\r
> 9= Kinetic En. 10= Total Energy 11= Temperature 12=Pressure
> (bar)\r
> 13= Vir-XX 14= Vir-XY 15= Vir-XZ 16= Vir-YX\r
> 17= Vir-YY 18= Vir-YZ 19= Vir-ZX 20= Vir-ZY\r
> 21= Vir-ZZ 22= Pres-XX (bar) 23= Pres-XY (bar) 24= Pres-XZ
> (bar)\r
> 25= Pres-YX (bar) 26= Pres-YY (bar) 27= Pres-YZ (bar) 28= Pres-ZX
> (bar)\r
> 29= Pres-ZY (bar) 30= Pres-ZZ (bar) 31= #Surf*SurfTen 32= Mu-X\r
> 33= Mu-Y 34= Mu-Z 35= T-Protein 36=
> Lamb-Protein\r" { send -- "5 7 0\r" }
> "End your selection with 0\r
> 1= LJ (SR) 2= Coulomb (SR) 3= Potential 4= Kinetic
> En.\r
> 5= Total Energy 6= Temperature 7=Pressure (bar) 8= Vir-XX\r
> 9= Vir-XY 10= Vir-XZ 11= Vir-YX 12= Vir-YY\r
> 13= Vir-YZ 14= Vir-ZX 15= Vir-ZY 16= Vir-ZZ\r
> 17= Pres-XX (bar) 18= Pres-XY (bar) 19= Pres-XZ (bar) 20= Pres-YX
> (bar)\r
> 21= Pres-YY (bar) 22= Pres-YZ (bar) 23= Pres-ZX (bar) 24= Pres-ZY
> (bar)\r
> 25= Pres-ZZ (bar) 26= #Surf*SurfTen 27= Mu-X 28= Mu-Y\r
> 29= Mu-Z 30= T-Protein 31= Lamb-Protein\r" { send --
> "2 0\r" }
> "End your selection with 0\r
> 1= LJ (SR) 2= Coulomb (SR) 3= Coul. recip. 4= Potential\r
> 5= Kinetic En. 6= Total Energy 7= Temperature 8=Pressure
> (bar)\r
> 9= Vir-XX 10= Vir-XY 11= Vir-XZ 12= Vir-YX\r
> 13= Vir-YY 14= Vir-YZ 15= Vir-ZX 16= Vir-ZY\r
> 17= Vir-ZZ 18= Pres-XX (bar) 19= Pres-XY (bar) 20= Pres-XZ
> (bar)\r
> 21= Pres-YX (bar) 22= Pres-YY (bar) 23= Pres-YZ (bar) 24= Pres-ZX
> (bar)\r
> 25= Pres-ZY (bar) 26= Pres-ZZ (bar) 27= #Surf*SurfTen 28= Mu-X\r
> 29= Mu-Y 30= Mu-Z 31= T-Protein 32=
> Lamb-Protein\r" { send -- "2 3 0\r" }
> eof exit
> }
> }
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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