From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sun May 02 2010 - 13:36:40 CDT
Hi Patrick,
Please do not take this explanation as 100% sure, but as you use only
distance colvar for two atoms, the OneSiteSystemForce shoud not be used.
Likely that this option could be used if you need projection of the (for
example) distance on the plain, or to obtain orthogonality of the each
of two set of atoms defining two colective variables.
Sincerely
Branko
On 5/1/2010 6:14 PM, Patrick Yee 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
>> }
>>
>>
>>
>> No virus found in this incoming message.
>> Checked by AVG - www.avg.com
>> Version: 9.0.801 / Virus Database: 271.1.1/2813 - Release Date: 04/15/10
>> 20:31:00
>>
>>
>>
>>
>
>
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 9.0.814 / Virus Database: 271.1.1/2847 - Release Date: 05/01/10 08:27:00
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:05 CST