Re: restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Nov 01 2008 - 17:33:10 CDT

Hi Sebastian,
this isn't a terribly helpful answer, but part of the reason you may not
be getting much of a response is that the old free energy module is not
used much anymore as far as I know; people tend to calculate
conformational pmfs using the abf module. Hopefully if someone is
familiar with these features they'll speak up.
Best,
Peter

Sebastian Stolzenberg wrote:
> Dear All,
>
> this is my 3rd e-mail on this subject:
> are PMF restarts actually possible at all?
> Or were my questions trivial?
>
> Thank you very much,
> Much Regards,
> Sebastian
>
>
> Sebastian Stolzenberg wrote:
>> Dear All,
>>
>> I am trying to restart a PMF calculation.
>> The freeEnergy script of my *very first* namd run was:
>>
>> ****************************
>> freeEnergyConfig {
>> urestraint {
>> dist pmf group { (A, 11) }
>> group { (A, 210) } kf=20, low=28.37,
>> hi=18.0
>> }
>> pmf {
>> task = grow
>> time = 1500 ps
>> print = 1 ps
>> }
>> pmf {
>> task = up
>> time = 15000 ps
>> }}
>> ****************************
>>
>>
>> For the restart,
>>
>> ****************************
>> freeEnergyConfig {
>> urestraint {
>> dist pmf group { (A, 11) }
>> group { (A, 210) } kf=20, low=27.644,
>> hi=18.0
>> }
>> pmf {
>> task = up
>> time = 13950 ps
>> print = 1 ps
>> }}
>> ****************************
>>
>>
>> 1.) Will this restart actually start at kf=20, or will I need to
>> introduce a "grow" phase again, so that it doesn't start at kf=0? The
>> output at step 1000 was lambdaKf=1.0 and lambdaRef=0.00007.
>>
>> 2.) What is "lambdaRef" by the way? Is this only for the logfile, or
>> does it have a physical meaning - do I need to reset it properly for
>> the restart, too? If yes, how?
>>
>> 3.) Is there any more documentation about pmf beyond the namd script,
>> so that I don't have to bug you guys with all these technical questions?
>>
>> Thank you,
>> Best,
>> Sebastian
>>
>>

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