From: dhacademic (dhacademic_at_gmail.com)
Date: Fri Sep 03 2010 - 12:30:57 CDT
Hi Jerome,
Thanks for the reply. According to your suggestion, I have tried "colvars"
in NAMD. But actually I feel quite confused about the colvars calculations.
There are a couple of questions about the parameters in colvars:
(1) The first two colvars are defined for distance restraint (my dist1colvar
and dist2colvar). In the distance restraint, the "lowerWallConstant" (or the
"upperWallConstant") imposes a potential centered on "lowerBoundary" (or the
"uperBoundary"), so the distance is restricted within the range. Does it
means that the "harmonic" bias type (the "distbias" in the following conf
file) is not necessary in this case?
(2) The third colvars is defined for RMSD (rmsdcolvar), where I want to
implement TMD by using colvars. In TMD, RMSD can gradually decrease to a
target value. Similarly, I specify the keywords of "targets 0.0" and
"targetsNumsteps 10000" in the harmonic restraint of colvars. But I'm not
clear weather it is correct. And I meet this problem after 10000 steps run:
TCL: Setting parameter colvars to on
FATAL ERROR: Setting parameter colvars from script failed!
(3) The histogram block is included in the colvars configuration file, but
no histogram information can be found in the output file.
Following is my namd configuration file for colvars and the corresponding
colvars.conf file. Can you please help to figure out what is wrong in these
files? Many thanks.
#### collective variables ####
colvars on
analysis on
colvarsConfig colvars.conf
#### colvars.conf ####
colvar {
name dist1colvar
distance {
atoms {
group1 {atomNumbers 100970}
group2 {atomNumbers 94229}
atomsFile colvar.pdb
}
lowerBoundary 3.4
upperBoundary 4.2
lowerWallConstant 10.0
upperWallConstant 10.0
width 0.1
outputAppliedForce on
}
name dist2colvar
distance {
atoms {
group1 {atomNumbers 107523}
group2 {atomNumbers 87680}
atomsFile colvar.pdb
}
lowerBoundary 3.4
upperBoundary 4.2
lowerWallConstant 10.0
upperWallConstant 10.0
width 0.1
outputAppliedForce on
}
}
colvar {
name rmsdcolvar
rmsd {
atoms {
atomNameResidueRange 386-485
psfSegID A
atomNameResidueRange 386-485
psfSegID B
atomNameResidueRange 386-485
psfSegID C
atomNameResidueRange 386-485
psfSegID D
atomNameResidueRange 628-763
psfSegID A
atomNameResidueRange 628-763
psfSegID B
atomNameResidueRange 628-763
psfSegID C
atomNameResidueRange 628-763
psfSegID D
}
refPositionsFile colvar.pdb
refPositionsCol O
refPositionsColvalue 5
lowerBoundary 4.0
upperBoundary 0.0
lowerWallConstant 1000.0
upperWallConstant 1000.0
outputAppliedForce on
}
}
harmonic {
name distbias
colvars dist1colvar dist2colvar
forceConstant 10.0
}
harmonic {
name rmsdbias
colvars rmsdcolvar
forceConstant 1000.0
targets 0.0
targetsNumsteps 10000
}
histogram {
outputFreq 10
On Tue, Aug 31, 2010 at 11:22 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> Hi,
>
> You could implement both TMD and the distance restraint as colvar
> biases - see "Collective Variable Calculations" in the user's guide.
>
> Cheers,
> Jerome
>
> On 31 August 2010 15:25, dhacademic <dhacademic_at_gmail.com> wrote:
> > Hi everyone,
> >
> > I meet this "FATAL ERROR: Due to a design error, GlobalMasterServer does
> not
> > support individual atom requests from multiple global force clients on
> > parallel runs" problem when I run TMD with TCL force. I have searched the
> > mail-list and found that someone else also had this problem. It seems
> that
> > two user defined forces (TMD and TCL force) can not be used at the same
> > time.
> >
> > In my system, TMD is applied for segment A and a distance restraint is
> > imposed for segment B (by using TCL force). In NAMD, is there any
> > alternative that can fulfill this requirement?
> >
> > Many thanks for any suggestion.
> >
> >
> >
>
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