Re: [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  wrote:

>  On 16/02/2012 3:14 PM, Juliette N. wrote:
>
>
>
> On 15 February 2012 23:05, Mark Abraham  wrote:
>
>>   On 16/02/2012 2:08 PM, Juliette N. wrote:
>>
>>
>>
>> On 15 February 2012 21:00, Mark Abraham  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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Thanks,
J. N.
-- 
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Plea

Re: [gmx-users] in vacu simulation

[Mark Abraham]

On 16/02/2012 3:14 PM, Juliette N. wrote:



On 15 February 2012 23:05, Mark Abraham > wrote:


On 16/02/2012 2:08 PM, Juliette N. wrote:



On 15 February 2012 21:00, Mark Abraham mailto:mark.abra...@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
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Re: [gmx-users] in vacu simulation

[Juliette N.]

On 15 February 2012 23:05, Mark Abraham  wrote:

>  On 16/02/2012 2:08 PM, Juliette N. wrote:
>
>
>
> On 15 February 2012 21:00, Mark Abraham  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.

>
> Mark
>
> --
> gmx-users mailing listgmx-users@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-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Thanks,
J. N.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] in vacu simulation

[Mark Abraham]

On 16/02/2012 2:08 PM, Juliette N. wrote:



On 15 February 2012 21:00, Mark Abraham > 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.


Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at 
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Re: [gmx-users] in vacu simulation

[Juliette N.]

On 15 February 2012 21:00, Mark Abraham  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). 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?

>
>
-- 
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Re: [gmx-users] in vacu simulation

[Mark Abraham]

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...


Mark

--
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Re: [gmx-users] in vacu simulation

[Justin A. Lemkul]

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.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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