Hi again Ross,
I read the documentation again. I think this random seed is related
with the ergodicity assumption on the system. If i assume my system is
ergodic, i can make an ensemble averaging over the replicas of the
system. For doing that i need to restart the calculation
with randomize velocities. More generally this should be randomize
positions and velocities but there are geometrical constraints etc, so
i can mostly randomize velocities. On the other hand, if i don't start
with ergodicity assumtion, i just need to restart the calculation
using last velocities and coordinates. This also means i am just doing
time averaging on the system and i assume time average may not be same
with ensemble average of trajectories. Specifically in my system,
according to previously taken NMR data, it looks like what i have is
rather similar to an attractor (in non-linear dynamics words, like
lorenz attractor). So now the question is; even if i don't assume
ergodicity, should i restart each run with randomize velocities ?
Again, should i use a different random number as a seed for those
starting velocities ?
all the best
peker
On Wed, Jan 26, 2011 at 9:41 PM, peker milas <pekermilas.gmail.com> wrote:
> Hi Ross,
>
> That was actually what i did. no ig option with ntt=3. but there was
> nothing about this, in tutorial. also in the manual it says, if ntx is
> less than 3 and initial temp does not equal to 0 velocities will
> depend on this seed. but my ntx is 7 and my initial temp is 300.0. on
> the other hand it effects the Andersen coupling ?? and that is not
> given in the tutorials ? this is confusing really. Should i start from
> beginning ? I mean i don't what i should say or ask...
>
> best
> peker
>
> On Wed, Jan 26, 2011 at 7:05 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>>> a minute). Then it stabilizes itself at this temperature. The actual
>>> simulation consists of many 500 pico second runs. I decided to use
>>> this time scale right after i had this NaN errors in the first time.
>>> My reasoning based on the observation of first set of NaN s in a
>>> longer run. Back in that time fine part of the .rst file was close to
>>> 800 pico seconds. Then this leads me to divide it into 500 pico second
>>> steps. Again for those runs, i am using a cutoff distance 10 A.
>>> iwrap=1 flag/options is included. But, I am not utilizing ig=-1
>>> flag/option. Basically my input file is exactly same with the input
>>> file
>>> in advanced web tutorial for explicit solvent case except this iwrap
>> option.
>>
>> "but I am not utilizing ig=-1"
>>
>> Don't do this..., unless you are setting the ig value manually to a
>> different value for each restart. If you are using ntt=3 this can be
>> disastrous.
>>
>> See: http://pubs.acs.org/doi/abs/10.1021/ct8002173
>>
>> All the best
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> ---------------------------------------------------------
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Adjunct Assistant Professor |
>> | Dept. of Chemistry and Biochemistry |
>> | University of California San Diego |
>> | NVIDIA Fellow |
>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
>>
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Received on Wed Jan 26 2011 - 22:30:02 PST
