[gmx-users] in vacu simulation

[Juliette N.]

Thanks. That was a new thing for me to learn.

On 15 February 2012 23:19, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

>  On 16/02/2012 3:14 PM, Juliette N. wrote:
>
>
>
> On 15 February 2012 23:05, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
>>   On 16/02/2012 2:08 PM, Juliette N. wrote:
>>
>>
>>
>> On 15 February 2012 21:00, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>>
>>> On 16/02/2012 12:22 PM, Justin A. Lemkul wrote:
>>>
>>>>
>>>>
>>>> Juliette N. wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am trying to run simulation in vaccum using the the changes shown
>>>>> below to the usual mdp file.
>>>>> pbc              =  no
>>>>>
>>>>> ;coulombtype         =  PME   ;vdw-type            =  Shift
>>>>> ;        Cut-offs
>>>>> rlist               =  0   rcoulomb     =  0
>>>>> rvdw              =  0
>>>>>
>>>>> nstlist             =  0               ns_type          =  simple
>>>>>
>>>>> Can anyone help me with some short questions please?
>>>>>
>>>>> 1- for pbc=no, I need to comment
>>>>>
>>>>> ;coulombtype         =  PME   ;vdw-type            =  Shift
>>>>> so it defaults to vdw-type =  Cut-off which are not suitable
>>>>> algorithms. Is using cut offs justified for in vacu runs?
>>>>>
>>>>>
>>>> Plain truncations in condensed-phase systems lead to artifacts.
>>>>  Neither of those conditions apply here, as you're using infinite cutoffs.
>>>>
>>>>
>>>>> 2- I am not clear about using infinite cutoffs. Why one refers to
>>>>> infinite cutoffs when
>>>>>
>>>>> rlist               =  0   rcoulomb     =  0
>>>>> rvdw              =  0     ?
>>>>>
>>>>> My understanding is that this settings means zero cutoff i.e no
>>>>> interaction is calculated. Why does this setting refer to infinite rc?
>>>>>
>>>>>
>>>>>
>>>> That's the way the code works.  There are various parameters that can
>>>> be set to -1, for instance, and that doesn't mean quantities are calculated
>>>> every -1 steps ;)
>>>>
>>>> Setting cutoffs to zero in this manner mean *all* interactions are
>>>> calculated, not none.  Prove it to yourself with a zero-step MD run.  The
>>>> nonbonded energy terms will not be zero, as they would in the case that no
>>>> interactions would be calculated.
>>>>
>>>>
>>>  Or read about pbc=no in manual section 3.4.9 like I suggested Juliette
>>> do earlier this week...
>>>
>>
>> Thanks Justin and Mark. I think you meant 7.3.9 which I did when you
>> referred me to that. My problem was that I did not expect rc=0  is *just
>> defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent
>> to no interaction than infinite cutff off (all interactions).
>>
>>
>>  Sure, but reading the documentation is usually a better idea than
>> making assumptions :)
>>
>> The underlying reason for this behaviour is that it is much easier for
>> the person writing the code to have one parameter that occasionally has a
>> "special" meaning when it takes a nonsense value (like rc<=0) then it is to
>> have a slew of parameters that have to be managed when they are input (and
>> checked, and documented) and then possibly passed through a cascade of
>> functions (lots of bureaucracy and chances to make errors) before they are
>> used. The alternative costs the programmer more time. In an ideal world
>> there would be an infinite amount of such time, but given the amount most
>> people are prepared to pay for scientific software, that time is severely
>> limited.
>>
>>
>>  And also I dont see why do we need to change rc to infinite. I mean if
>> force fields dictate cutoffs based on a distance where nonbonded
>> interactions are close enough to zero (negligible), what  purpose use of
>> infinite cutoff serve?
>>
>>
>>  Efficiency, like I said in the first post in this thread. Given that
>> your force field was parametrized with given cut-offs for the condensed
>> phase, to what purpose do you wish to calculate in vacuo? The perturbation
>> from calculating in vacuo will be much larger than the perturbation from
>> the use of infinite cut-offs.
>>
>
>
> Thank you. I am looking at potential of a single molecule in vacu for heat
> of vap purposes at different temperatures by changing ref_temp and gen_temp
> for each run.
>
>
> So it's much more bureaucracy every nstlist>0 steps to take your N atoms
> and look at their distance from the other N-1 atoms and make lists of which
> ones are inside rc than it is to just compute them all every step and know
> that if they're further than rc then the effect is tiny. For small enough
> N, the later is guaranteed to be faster...
>
> Mark
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Thanks,
J. N.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120215/7aae255a/attachment.html>