Thank you,
I understand that includes equilibration, heating everything which has ntt=3 ?
So why for example in tutorial 3 section two there is this example:
~prod ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Which obviously does not use ig at all?
Thansk a lot,
Fabian
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 21 Dec 2015, at 3:20 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Dec 21, 2015, Fabian gmail wrote:
>>
>> Maybe I have a trivial question, but I would like to know if I do run 10
>> ns in say 5 x 2 ns runs, I guess I need to use ig = -1 only in the first
>> one or in the equilibration stage only to get different samplings for
>> let’s say 3 different such full runs (min + equil + prod) correct?
>
> If you are using the Langevin thermostat (ntt=3), you should *always* set
> ig=-1. If you are doing a restart calculation and using ntt=0 or 1, then the
> value of ig becomes irrelevant.
>
> ....dac
>
>
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Received on Mon Dec 21 2015 - 06:00:04 PST
