VMD-L Mailing List
From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Mon Jan 30 2017 - 09:06:14 CST
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Hi all,
thanks Jerome and Giacomo for quick replies. For clarity's sake I report
the colvar_grid.txt below:
colvarsTrajFrequency 100 # output values every 100 steps
colvar {
name DistLeu83
lowerBoundary 0
hardLowerBoundary on
upperBoundary 35
upperWall 35
upperWallConstant 800
expandBoundaries on
width 1
distance {
group1 {
atomNumbers 5048
}
group2 {
atomNumbers 1373
}
}
}
colvar {
name angle
lowerBoundary 0
hardLowerBoundary on
upperBoundary 180.0
hardUpperBoundary on
expandBoundaries off
width 10
angle {
group1 {
atomNumbers 1373
}
group2 {
atomNumbers 5048
}
group3 {
atomNumbers 5031
}
}
}
metadynamics {
colvars DistLeu83 angle
hillWeight 0.6
newHillFrequency 1000
wellTempered on
biasTemperature 890
hillWidth 1.25
writeFreeEnergyFile on
rebinGrids on
}
If I am not missing something (which is much more than possible) I should
not have enabled that option, unless it comes embedded in some other
options as well. What seems weird (at least to me) is that I used the very
same script with the same colvar_grid.txt file with a compiled version of
vmd some months ago, and it worked; then I switched to version 1.9.3 and I
encountered this problem.
Thanks again,
Stefano
2017-01-30 15:49 GMT+01:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> Hi Stefano, do you have outputTotalForce enabled in the config file
> colvar_grid.txt?
>
> If so, please disable it because VMD does not support calculation of
> atomic forces.
>
> Giacomo
>
> On Sun, Jan 29, 2017 at 6:40 PM, Stefano Guglielmo <
> stefano.guglielmo_at_unito.it> wrote:
>
>> Dear vmd users,
>>
>> I am trying to calculate the energy of each frames of a trajectory
>> generated by NAMD in a metadynamics simulation; for this purpose I have
>> written the following tcl script:
>>
>> package require bigdcd
>> proc metadynamics_energy { frame } {
>> global all
>> if {$frame == 1} {
>> cv molid 0
>> cv configfile ../colvar_grid.txt
>> cv load ../cdk_8bS_pocket_metadyn_75ns_replica1
>> }
>> cv update
>> set energy [cv bias metadynamics1 energy]
>> puts "$frame: $energy"
>> }
>> set mol [mol new ../cdk2_8bS_pocket_wb_ion.psf type psf waitfor all]
>> set all [atomselect $mol all]
>> $all global
>> bigdcd metadynamics_energy auto ../cdk_8bS_pocket_metadyn_75ns
>> _replica1.dcd
>> bigdcd_wait
>> quit
>>
>> When I source the script in vmd I got the following error message:
>>
>> bigdcd aborting at frame 1
>> Error: total forces are currently not implemented.
>> Error loading state file
>> bigdcd_done
>> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
>> Info) Exiting normally.
>>
>> Does anyone have suggestions?
>>
>> Thanks in advance
>>
>> Stefano
>>
>> --
>> Stefano GUGLIELMO PhD
>> Assistant Professor of Medicinal Chemistry
>> Department of Drug Science and Technology
>> Via P. Giuria 9
>> 10125 Turin, ITALY
>> ph. +39 (0)11 6707678
>>
>>
>
-- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707678
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