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

From: Giacomo Fiorin (
Date: Thu Oct 22 2020 - 15:45:17 CDT

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.


On Thu, Oct 22, 2020 at 4:14 AM zeynab hosseini <>

> Hi Giacomo,
> On Wed, Oct 21, 2020 at 3:09 PM Giacomo Fiorin <>
> 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 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)--000000000000df3ac905b2488c87--

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