From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Fri May 01 2015 - 11:18:21 CDT
Yes. Some might say that you can write a small tcl proc to parse an old
log file and figure out that number "automatically"... but it all
depends on how strongly you need this "automation" :)
On 05/01/2015 10:16 AM, Phillips, Carolyn L. wrote:
> Thanks Maxim
>
> Does firsttimestep need to be set manually to the correct value then?
>
> Carolyn
>
> Sent from my iPhone
>
>> On May 1, 2015, at 10:46 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>>
>> Carolyn,
>>
>> NAMD behavior depends on how you actually "ramp up" the temperature and what you mean by "restart automatically". If you use "reassignTemp/reassignFreq/reassignIncr/reassignHold" in conjunction with "firsttimestep" then NAMD should restart with correct temperature. If you use your own tcl script along with "rescaleTemp", then you have to take care of everything yourself.
>>
>> "restartsave" does not do anything special in this regard as it only allows you to restart a simulation from an arbitrary point in the past and requires a little bit of tcl scripting.
>>
>> Maxim
>>
>> P.S. "firsttimestep" should be set to the last step in the halted/aborted simulation at which NAMD wrote restart files.
>>
>>
>>> On 04/30/2015 06:51 PM, Phillips, Carolyn L. wrote:
>>> I apologize if this has been answered before but searching the user list + manual has not answered this for me.
>>>
>>> I want to do a simulated annealing of a system. It would seems this can be done by temperature reassignment. However, I also am working with a wallclock limit that means I need to restart my simulation with fairly high frequency. What I cannot figure out is whether NAMD can correctly return to the specified temperature schedule when restarted automatically. For example, if the temperature is ramping from 300K to 350K by incrementing by 10K every 1000 time steps, and the simulation is restarted after 20001 time steps, will the temperature of the system revert to 300K or be at 320K? If I use “restartsave yes” does that do anything?
>>>
>>> Cheers,
>>> Carolyn
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