VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Feb 02 2017 - 21:21:19 CST

Hi Stefano, if I sort the contents of the PMF file according to the energy
I get that the lowest free-energy values are:
 2.5 115 -0
 3.5 125 0.0138202
 3.5 115 0.23787
..

If I sort the last part of the "output" file, and look for the largest
values of the metadynamics potential I get:
..
2985 2.65351685319544e+00 1.14605320428208e+02 11.4118
2987 2.70255164664564e+00 1.12710621783704e+02 11.4129
3737 3.74336457789873e+00 1.21202158456548e+02 11.4188

So, again, the putative free-energy minimum is in the neighborhood of
distance = 3 Å, angle = 120°. Clearly the PMF has a grid with round values
for the two variables and the trajectory does not, but that's the only
difference that I can see.

Giacomo

On Thu, Feb 2, 2017 at 8:04 PM, Stefano Guglielmo <
stefano.guglielmo_at_unito.it> wrote:

> Hi Giacomo,
>
> to be honest, I am missing the use of "cv save" to write a pmf file...
> besides this, I had a look at the file, generated in vmd, reporting
> metadynamics potential for each frame (and the corresponding values of the
> two colvars I defined) and I found the inconsistency I wrote in the
> previous post: the "configuration" corresponding to the 0 in the pmf
> generated in NAMD is not the one with the largest value of metadynamics
> potential; moreover I could not find the numerical relationship between
> metadynamics potential and pmf: does this behavior depend on somewhat wrong
> choice of colvars or bias parameters?
> The two files are attached with the second reporting frames
> distance angle energy.
>
> Stefano
>
> 2017-02-01 15:43 GMT+01:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>
>> Hi Stefano, besides the obvious issue that the metadynamics potential
>> converges to the negative of the PMF, can you try using the cv save
>> command in VMD, to write a PMF file?
>>
>> This file could then be compared to the one written by NAMD (which you
>> already have), and detect any inconsistencies.
>>
>> Giacomo
>>
>> On Tue, Jan 31, 2017 at 9:02 PM, Stefano Guglielmo <
>> stefano.guglielmo_at_unito.it> wrote:
>>
>>> Hi all,
>>>
>>> For sure I am missing something but I've got a bit confused about the
>>> discrepancy between the pmf minimum obtained from a metadynamics simulation
>>> (ie the colvars values corresponding to 0) and the minimum value of
>>> metadynamics potential calculated for the same simulation through vmd
>>> colvars module, corresponding to quite different values of colvars compared
>>> to the previous ones.
>>> Can anybody give some hints or references?
>>>
>>> Thanks in advance
>>>
>>> Stefano
>>>
>>> --
>>> Stefano GUGLIELMO PhD
>>> Assistant Professor of Medicinal Chemistry
>>> Department of Drug Science and Technology
>>> Via P. Giuria 9
>>> 10125 Turin, ITALY
>>> ph. +39 (0)11 6707678
>>>
>>>
>>
>
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707678
>
>