Re: [AMBER] NaN error in .rst files

From: peker milas <>
Date: Wed, 26 Jan 2011 22:07:34 -0800

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

On Wed, Jan 26, 2011 at 9:41 PM, peker milas <> 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 <> 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:
>> All the best
>> Ross
>> /\
>> \/
>> |\oss Walker
>> ---------------------------------------------------------
>> |             Assistant Research Professor              |
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Received on Wed Jan 26 2011 - 22:30:02 PST
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