Re: ABF non-uniform sampling

From: Patrick Yee (pyee_at_nd.edu)
Date: Sat May 01 2010 - 11:14:52 CDT

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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