From: Canal de Sebassen (thecromicusproductions_at_gmail.com)
Date: Sat Nov 09 2019 - 19:03:01 CST
Thanks for your reply, Giacomo. I'll take your suggestions into
consideration when setting up the system.
Regards,
Sebastian
On Thu, Nov 7, 2019 at 6:37 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Canal, first of all try upgrading to the latest NAMD nightly build.
> Thanks to Jim's help, I added extra checks that make the input/output
> functionality more robust (the same checks are used when writing the NAMD
> restart files):
> https://github.com/Colvars/colvars/pull/276
> There is also an important bugfix in the output of the PMF (the restart
> files are fine):
> https://github.com/Colvars/colvars/pull/259
>
> About the exchange rate, on modern hardware optimal performance is around
> few milliseconds/step, so 1000 steps is kind of short for a full cycle with
> all replicas reading each others' files. Best to increase it by a factor
> of 10 or more: I would have made its default value the same of the restart
> frequency, but there is no telling how long that would be for each user's
> input.
>
> Regarding the PMFs, nothing special is needed. Each replica will write
> PMFs with the same contents (the PMF extracted from the shared bias), so
> they will be equal minus the fluctuations arising from synchronization.
> You are probably confused by the partial output files, which are triggered
> by dumpPartialFreeEnergyFile (a flag that is off by default).
>
> Lastly, Gaussians 0.01 kcal/mol high added every 100 steps is quite a bit
> of bias, and will be further multiplied by the number of replicas.
>
> Giacomo
>
> On Thu, Nov 7, 2019 at 6:06 PM Canal de Sebassen <
> thecromicusproductions_at_gmail.com> wrote:
>
>> Hello,
>>
>> Say I run a metadynamics simulation with 10 walkers. I then get 10
>> different pmf files. If my simulation was in 2D, how do I get a single
>> energy landscape? Do I use abf_integrate?
>>
>> Also, what are some good practices when running these kind of simulations?
>> I haven't found many examples. This is one my current colvars files. I
>> plan to get about 1-5 microseconds of data. Is a replicaUpdateFrequency of
>> 1000 too large? I tried with a smaller one but I get problems because some
>> files of a replica cannot be found by another one (maybe due to lagging?).
>>
>> Thanks,
>>
>> Sebastian
>>
>> colvarsTrajFrequency 100
>>
>> colvar {
>>
>> name d1
>>
>> outputAppliedForce on
>> width 0.5
>>
>> lowerBoundary 0.0
>> upperBoundary 30.0
>>
>> upperWallConstant 100.0
>>
>> distanceZ {
>> forceNoPBC yes
>> main {
>> atomsFile labels.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> ref {
>> atomsFile labels.pdb
>> atomsCol B
>> atomsColValue 2.0
>> }
>> }
>> }
>>
>> colvar {
>>
>> name d2
>>
>> outputAppliedForce on
>> width 1
>>
>> lowerBoundary 0.0
>> upperBoundary 10.0
>>
>> upperWallConstant 100.0
>>
>> coordNum {
>> cutoff 4.0
>>
>>
>> group1 {
>> atomsFile labels.pdb
>> atomsCol O
>> atomsColValue 1.0
>> }
>> group2 {
>> atomsFile labels.pdb
>> atomsCol B
>> atomsColValue 2.0
>> }
>> }
>> }
>>
>>
>>
>>
>>
>> metadynamics {
>> colvars d1 d2
>>
>> useGrids on
>> hillWeight 0.01
>> newHillFrequency 100
>> dumpFreeEnergyFile on
>> dumpPartialFreeEnergyFile on
>> saveFreeEnergyFile on
>> writeHillsTrajectory on
>>
>> multipleReplicas yes
>> replicaID rep1
>> replicasRegistry replicas.registry.txt
>> replicaUpdateFrequency 1000
>> }
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
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