Re: Volumetric map simulations

From: Vermaas, Josh (
Date: Thu Mar 25 2021 - 09:33:17 CDT

Hi Carlo,

What is in the beta column? You are using the occupancy column to determine if the atoms should be coupled to the potential or not. But the "weight" for each atom also matters. For traditional grid forces, when it was being used to apply an electric field, folks would copy the atomic charges to the beta column so that a carbon and hydrogen atom wouldn't feel the same attractive force. MDFF folks will use the mass of the element. The point being, is that your beta column can't be zero, otherwise it doesn't contribute to the gridforce value colvars is depending on. If you just want to count waters, I *think* the correct thing is to have the "noh and water" have a 1 in the beta column. You should then see non-zero values for the colvar.


On 3/25/21 6:22 AM, Carlo Guardiani wrote:
Dear NAMD experts,
I am trying to run simulations with volumetric map-based
variables. At the moment I am trying to bias the number
of water molecules inside the pore of an ion channel
following the instructions in the Reference manual for
the Collective Variables Module. I built the pore occupancy
map using VMD on a preliminary trajectory

set sel [atomselect top "water and (z > -40) and (z < 25) and (sqrt(x*x+y*y) < 12)"]

volmap occupancy $sel -allframes -combine max -o Occupancy.dx

package require volutil

volutil -o Occupancy_smooth.dx -pad -smooth 0.0001 Occupancy.dx

The map, visualized with VMD, looks reasonable in that all
the pore region appears to be filled.

Following the manual, I also created a file where all water
molecules are marked in the occupancy column. Is that correct ?
Maybe I had to mark only the water molecule initially inside the
pore ? The file was generated with the following tcl script

mol load pdb TMD_4HKR_to_6BBF_frame_0.pdb
set all [atomselect top "all"]
$all set occupancy 0
set wat [atomselect top "water and (name O)"]
$wat set occupancy 1
$all writepdb mark_water.pdb

I added the following commands to the main NAMD input file

mGridForce yes
mGridForcePotFile Cavity Occupancy_smooth.dx
mGridForceFile Cavity mark_water.pdb
mGridForceCol Cavity O
mGridForceChargeCol Cavity B
mGridForceScale Cavity 0.0 0.0 0.0

colvars on
colvarsConfig ./ColvarConfig.conf

Finally, I defined in file ColvarConfig.conf a collective
variable that, I expected, should count the number of water
molecules in the cavity.

colvar {
   name nwaters
   mapTotal {
    mapName Cavity
    componentCoeff 1.0

harmonic {
  colvars nwaters
  centers 277 # centered around initial number of water molecules
  forceConstant 50000

As you can see, I applied an harmonic bias to keep the number
of water molecules in the cavity close to the initial value
(277 molecules). Here comes the problem: according to the
.traj file the value of collective variable nwaters is constantly
equal to zero which is clearly wrong. The system was run for 5.0 ns
with NAMD 2.14. During the simulation the number of water molecules
inside the pore made oscillations of the order of 10% with respect
to the initial value. However, I suspect that an unbiased equilibrium
simulation would have done the same, so that this cannot be used as
a diagnostic criterium that the simulation is doing what it was
intended to do.

Could you please tell me what to do ? This is the first time I run this
kind of simulations so that some trivial mistake is highly possible.

Many thanks for your help,

Carlo Guardiani

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Josh Vermaas
Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology<>;!!DZ3fjg!vf1OksGrvmaNdGhfe05Ths_wW2XkImtUO-ap3ohAbsjbYDwiTZu5jMMDfiw4w_hyKw$ 

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