Re: well-tempered metadynamics deforms the water box and the system becomes unstable..

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Fri Oct 23 2020 - 04:21:33 CDT

Hi Giacomo,

Thank you for your help and consideration sincerely.

All the best,
Zeynab

On Thu, Oct 22, 2020 at 4:45 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hi Zeynab, that sounds good. I do not think you need 2.14 if it is a
> problem to install it. As I mentioned, the effect of adding it is
> minimal. It would be more pronounced if you were e.g. doing constant pH
> and running many short run commands, but even then the effect would be
> simply adding the bias at a higher rate, but the bias would be always
> accounted for.
>
> Giacomo
>
>
> On Thu, Oct 22, 2020 at 4:14 AM zeynab hosseini <
> hosseinizeynab93_at_gmail.com> wrote:
>
>> Hi Giacomo,
>>
>> On Wed, Oct 21, 2020 at 3:09 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> wrote:
>>
>>> Hi Zeynab, thanks for checking.
>>>
>>> I presume that you generated this using a NAMD prior to 2.14. There
>>> should not be two Gaussian hills added at the same step, i.e. step 500000.
>>> The Colvars version included in NAMD 2.14 corrects for this error.
>>>
>>
>> Yes you are right. I performed the test on the cluster machine on which
>> the NAMD version 2.13b1 is installed. I‚ÄĆ have to ask the helpdesk to
>> install the 2.14 version.
>>
>>>
>>> Given your setup the error results in one extra Gaussian hill added
>>> every 2000 hills, which on average is similar to using 0.1 * 2001/2000 =
>>> 0.10005 kcal/mol as initial weight. I don't think that this will affect
>>> convergence significantly for as long as you are adding the bias slowly
>>> enough to get a PMF (either with standard metadynamics or well-tempered).
>>>
>>> The second hill is slightly smaller than the previous one due to the
>>> well-tempered scaling, so that is fully expected.
>>>
>>
>> Here is the result of new test with 2.14 which seems everything is OK:
>> - tail cnt-ser_meta_*29*.colvars.meta-distance.hills.traj
>> 499250 2.35892630640388e+01 4.00000000000000e-03
>> 8.04196673987633e-02
>> 499500 2.26889661523101e+01 4.00000000000000e-03
>> 9.33115557260331e-02
>> 499750 2.31630224461575e+01 4.00000000000000e-03
>> 3.87756645748246e-02
>> 500000 2.30916666324611e+01 4.00000000000000e-03
>> 4.50554516054642e-02
>> - head cnt-ser_meta_*30*.colvars.meta-distance.hills.traj
>> 500250 2.29872034711264e+01 2.00000000000000e-03
>> 6.01328206388017e-02
>> 500500 2.34327307021109e+01 2.00000000000000e-03
>> 2.90463979184289e-02
>> 500750 2.31268698406103e+01 2.00000000000000e-03
>> 2.69021176213748e-02
>> 501000 2.31385369258797e+01 2.00000000000000e-03
>> 2.65591196168166e-02
>>
>> Thanks a lot for your kind help.
>>
>> All the best,
>> Zeynab
>>
>

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