Re: Dihedral colvar

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Sep 08 2017 - 14:54:44 CDT

Trying to create multiple variables with the same name will give an error
message that is self-explanatory. I say that so that you won't ask for
help later on this particular problem.

As for colvarsConfig being a required option, that's from a much version of
NAMD (before 2.11 at least). Please upgrade or write a dummy file for
colvarsConfig as a workaround.

In the future, please keep in mind that any assistance from the NAMD
mailing list is for the latest version of the code.

Giacomo

On Fri, Sep 8, 2017 at 3:33 PM, PRITI ROY <priitii.roy_at_gmail.com> wrote:

> Thanks for your suggestion. The NAMD error is as follows:
>
> TCL: Suspending until startup complete.
> ERROR: 'colvarsConfig' is a required configuration option
> ERROR: when 'colvars' is set
> ERROR: colvarsConfig defines: configuration for the collective variables
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
> So if i set this option then in the the hoe to by-pass the value from NAMD
> to colvar configuration file?
>
> Best,
> Priti
>
>
> On Sat, Sep 9, 2017 at 12:36 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
>> I can see at least one mistake at the end. Your name and colvars values
>> within the harmonic are flipped. Not to mention you are creating a ton of
>> colvars and harmonics with the same name, and I'm pretty sure that leads to
>> unintended consequences. Just an FYI, you are going to have alot more
>> success if you provide the error message NAMD provides and at least try to
>> parse it yourself. Saying something "is not working" creates alot of work
>> for the folks who would like to help you.
>> -Josh
>>
>> On 09/08/2017 01:01 PM, PRITI ROY wrote:
>> Dear Jerome,
>>
>> Thank you again for giving such information. Now I have used the "tcl"
>> in NAMD input file for colvar and create such type of colvar string as you
>> told previously. But still this is not working. Can you please check the
>> script which I copied in below where I might did some mistake.
>>
>> ####NAMD input file
>> structure ../../c_ion.psf
>> coordinates ../../c_ion.pdb
>> outputname min01 #writes final .vel and .coor
>>
>> paraTypeCharmm on #parameter file is charmm type
>> parameters /home/nsengupta/priti/restrain/par_all22_prot.prm
>>
>> exclude scaled1-4 #which pair is excluded from non-bonded
>> inter
>> 1-4scaling 1.0
>> cutoff 12.5 #coulomb and vdW in Angs
>> switching on #smoothing function for coulomb and vdW
>> switchdist 10.5 #distance at which smooth starts (in Angs)
>> pairlistdist 13.5 #goes with cutoff
>>
>> timestep 2.0 #timesteps are in femtoseconds
>> rigidBonds all ;# needed for 2fs steps
>> nonbondedFreq 1 #time steps between non-bonded evaluation
>> restartfreq 1 #at this frequency
>> dcdfile min01.dcd #writes .dcd file
>> dcdfreq 500 #at this frequency
>> outputEnergies 500 #writes energy at this frequency
>> fullElectFrequency 2 #time steps between Coulomb evaluation
>> stepspercycle 20 #atoms are reassigned every cycle
>>
>> PME on #use particle mesh Ewald for Coulomb
>> PMEGridSpacing 1.0
>>
>> cellBasisVector1 118.0 0.0 0.0 #periodic boundary
>> cellBasisVector2 0.0 76.0 0.0 #conditions
>> cellBasisVector3 0.0 0.0 89.0
>> cellOrigin 232.49 80.76 7.22
>>
>>
>> minimization on
>> numsteps 20000
>>
>> colvars on
>>
>> ###file opening containg atom index and phi/psi value
>> set f1 [open "c_A.dat" r] #atom C index
>> set ff1 [read $f1]
>> set f2 [open "n_A.dat" r] #atom N index
>> set ff2 [read $f2]
>> set f3 [open "ca_A.dat" r] #atom CA index
>> set ff3 [read $f3]
>> set f4 [open "phi1_a.dat" r] #phi value
>> set ff4 [read $f4]
>>
>> for {set n 0} {$n <= 54} {incr n} {
>> set nxt [expr ($n + 1)]
>>
>> #phi
>> set c1_p [lindex $ff1 $n]
>> set n_p [lindex $ff2 $n]
>> set ca_p [lindex $ff3 $n]
>> set c2_p [lindex $ff1 $nxt]
>> set p [lindex $ff4 $n]
>>
>> cv config "colvar {
>> name phi
>> dihedral {
>> group1 {
>> atomNumbers $c1_p
>> }
>> group2 {
>> atomNumbers $n_p
>> }
>> group3 {
>> atomNumbers $ca_p
>> }
>> group4 {
>> atomNumbers $c2_p
>> }
>> }
>> }"
>>
>> harmonic {
>> name phi
>> colvars dihedral
>> centers $p
>> forceConstant 5.0
>> }
>> }
>>
>>
>> Best,
>> Priti
>>
>> On Fri, Sep 8, 2017 at 7:23 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr
>> <mailto:jerome.henin_at_ibpc.fr>> wrote:
>> The cv command is available both in NAMD and VMD, once you've enabled the
>> colvars module.
>>
>> You cannot use Tcl scripting within a colvars configuration file - you
>> can use it in the NAMD config file to generate colvars configuration
>> strings as in the example I gave above.
>>
>> Jerome
>>
>> On 8 September 2017 at 15:44, PRITI ROY <priitii.roy_at_gmail.com<mailto:
>> priitii.roy_at_gmail.com>> wrote:
>> Dear Jerome,
>>
>> Thank you for your fast reply. According to your script the "cv" command
>> is accesible in vmd as per I know or I might be completely not understand
>> well. If possible give some insights.
>> I have written one tcl colvar configuration file using four types atom
>> index which were saved in ".dat" file and run in loop. But when I run this,
>> error shoing that "keyword "set" is not supported". Does "tcl" not
>> accessible to colvar?
>>
>> Kindly enlighten this matter.
>>
>> Best,
>> Priti
>>
>>
>> On Mon, Sep 4, 2017 at 6:10 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr
>> <mailto:jerome.henin_at_ibpc.fr>> wrote:
>> Hi Priti,
>>
>> If I understand you correctly, you want to define a series of 50 dihedral
>> restraints. You will need to define one separate colvar for each angle, but
>> you don't have to write them separately. That can be scripted using a Tcl
>> loop:
>>
>> for {set i 0} { $i < 50 } {incr i} {
>> cv config "colvar { dihedral ... }"
>> }
>>
>> Where the colvar block contains the details of the dihedral angle. You
>> can use variable $i inside the block to define the specifics of each angle.
>>
>> Best,
>> Jerome
>>
>> On 4 September 2017 at 13:08, PRITI ROY <priitii.roy_at_gmail.com<mailto:
>> priitii.roy_at_gmail.com>> wrote:
>> Dear all,
>>
>> I would like to do dihedral restrain using the colvar module of nearly 50
>> residues. I have gone through the colvar module. In dihedral colvar, there
>> are four group selection which are for atoms and depending on 1st group it
>> denote the particular dihedral angel. Basically this module describe in
>> light of atoms.
>>
>> How could I define this dihedral colvar for residues?
>>
>> Please give some idea to resolve my problem.
>>
>> Thanks,
>> Priti
>>
>>
>>
>>
>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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