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 |
> ---------------------------------------------------------
>
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Received on Wed Jan 26 2011 - 22:00:03 PST
