From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Mon Nov 22 2021 - 03:58:09 CST
Thanks for the suggestion. Based on your reply I have written an ad hoc tcl
script for the same purpose (it harmonically constrains the com of bilayer
and first few non titratable residues of protein ) but during run time the
script crashes with unknown tcl error. Any help regarding this error will
be highly appreciated.
script snippet :
tclForces on
tclForcesScript {
set k 0.05
set r0 9.847
# com of bilayer
set group1 [addgroup {13 143 266 389 519 649 779 909....}]
# com of amp
set group2 [addgroup {15367 15369 15381 15382..}]
print "starting proc"
print "-------------"
proc calcforces {} {
print "inside proc"
print "changing scope of variables"
# set change variable
global group1 group2 k r0
# load coordinates
loadcoords c
# get z coords of both groups
set r1 [$c(1)]
set r2 [$c(2)]
foreach {x1 y1 z1} $r1 {}
foreach {x2 y2 z2} $r2 {}
set r_z [expr {$z2-$z1}]
set disp [expr {$r_z-$r0}]
# optional add energy - will be displayed in MISC
# addenergy [expr {$k*$disp*$disp/2.0}]
# calculate force
set force [expr {-$k*$disp}]
addforce $group1 $force
addforce $group2 [expr {-1.0*$force}]
}
# close proc calcforces
# deleting all atomslections
clearconfig
}
In logfile the error encountered was :
Info: Startup phase 10 took 6.5302e-05 s, 324.613 MB of memory in use
Info: Startup phase 11 took 0.000188028 s, 324.613 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 12 took 0.000182779 s, 324.613 MB of memory in use
Info: CREATING 1104 COMPUTE OBJECTS
TCL: starting proc
TCL: -------------
TCL: parameter unknown for NAMD config parameter
FATAL ERROR: Unknown Tcl error
On Sat, 20 Nov 2021 at 21:55, Brian Radak <brian.radak_at_gmail.com> wrote:
> This is unfortunately an unsolved problem. As you point out - the atom
> indices change during a CpHMD simulation and so the selections would need
> to be updated at each cycle (probably with a bit of bookkeeping). One thing
> that can be exploited is that the number of residues does not change, so if
> it is possible to use residue and name based selections, that should work.
>
> In previous work where we used restraints we took advantage of the fact
> that it was only a single residue that was titrating and so all indices
> above the atom sidechain are fixed during the simulation (a bit of a hack).
>
> To be honest, it might be easier for someone to implement restraints based
> on a selection syntax rather than solve the indexing problem that is
> specific to CpHMD.
>
> HTH,
>
> BKR
>
>
> On 11/20/21 12:29 AM, Diship Srivastava wrote:
>
> Hi,
> I am currently working on insertion of an antimicrobial peptide (AMP) on
> bilayer membrane using constant pH MD. I am trying to constrain the center
> of mass of AMP and membrane, while cphmd is active. Since cphmd doesn't
> have colvar support and number of atoms during cphmd changes during the
> run, both colvars and constraints result in fatal error during the job. How
> can I constrain the com under cphmd conditions?
>
> Thanks in advance.
>
>
>
>
> --
> Diship Srivastava
> SRF
> Department of Chemistry
> IIT(ISM) - Dhanbad
> India
>
>
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