From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Sat May 01 2010 - 14:37:22 CDT
Hi Patrick, OneSiteSystemForce will make the total forces on the colvar be
computed only from the total forces of "group1", instead of all groups of
atoms involved. This reduces the size of the statistical sample, and hence
may affect the rate of convergence of your result: but once you converge,
the limiting distribution of forces and the PMF are just the same as when
you don't use the flag.
You should use it to decouple certain colvars or colvar components from the
others, so that the ABF scheme as it is implemented in NAMD can rely on the
orthogonality of their gradients to compute their total forces.
If you are using only one colvar, or multiple colvars acting on different
groups of atoms, I don't think it's an advantage to use it.
Giacomo
---- ----
Giacomo Fiorin
ICMS - Institute for Computational Molecular Science
Temple University
1900 N 12 th Street, Philadelphia, PA 19122
mail: giacomo.fiorin_at_gmail.com
---- ----
On Sat, May 1, 2010 at 12:14 PM, Patrick Yee <pyee_at_nd.edu> wrote:
> Thank you both for your advice,
>
> I managed to get the system working. I have one more quick question -
>
> If I'm performing ABF simulations on molecules that consist of about
> 20 atoms, will I want to use the OneSiteSystemForce parameter? I am a
> little confused on how this parameter would change a PMF. Thank you.
>
> Patrick
>
>
> On Fri, Apr 16, 2010 at 6:04 AM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> > Hi Patrick,
> >
> > Maybe significant lower value of `Colvarstrajfrequency`, next `analysis
> > on`, than `hideJacobian no', 'applyBias yes' will be helpfull (even
> > some of directives are applied by default). Also, did you use PME and
> PBC.
> > If you used PBC how you treat hydrogens`.
> >
> > Sincerely
> >
> > Branko
> >
> >
> >
> >
> >
> >
> >
> > On 4/16/2010 5:19 AM, Patrick Yee wrote:
> >
> > Hi NAMD users,
> >
> > I am having a problem with non-uniform sampling using ABF and colvars.
> > I did not have these sampling problems when using the TCL scripts for
> > ABF in NAMD 2.6. My sampling increases fairly linearly until the
> > simulation ends and even long simulations (10-20 ns) did not have
> > uniform sampling. Does anyone have any idea of why the sampling is not
> > uniform? I've given more details below.
> >
> > I've just started using colvars (instead of the NAMD 2.6 TCL scripts)
> > for calculating a PMF with the ABF method. To test if the PMF would
> > work on my systems when I used the TCL script ABF method, I first
> > tried finding the PMF on pair of methane molecules in water and then
> > on Na+ and Cl- ions in water (the latter being from the tutorial); the
> > results matched very closely what I'd found from other MD simulations.
> > When I tried these same simulations in NAMD 2.7b2 with colvars, I
> > didn't get the correct PMF as I had using ABF with TCL scripts, most
> > likely because the sampling is not becoming uniform as the simulation
> > progresses. Note that with colvars I used fullSamples = 500, which was
> > the same as with the TCL script. I also thought the simulation might
> > not have been allowed to proceed long enough, but even after 10
> > million steps at 1fs/step, the sampling was very non-uniform. Sampling
> > ranges from 40000 when the groups are close and moves fairly linearly
> > to about 25000 as the groups move apart. I attached the colvars input
> > file I am using below. Again, please tell me why the sampling is not
> > becoming uniform.
> >
> > Thank you in advance for your help.
> >
> > Colvarstrajfrequency 2000
> >
> > colvar {
> >
> > name IonDistance
> > width 0.1
> > lowerboundary 0.05
> > upperboundary 13.00
> > lowerwallconstant 10
> > upperwallconstant 10
> >
> > distance {
> > group1 {
> > atomnumbers { 1 }
> > }
> > group2 {
> > atomnumbers { 2 }
> > }
> > }
> > }
> >
> > abf {
> > colvars IonDistance
> > fullSamples 500
> > }
> >
> >
> >
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> > 20:31:00
> >
> >
> >
>
>
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