Re: [gmx-users] Heat of vap

[David van der Spoel]

On 2011-04-04 01.32, Justin A. Lemkul wrote:



Elisabeth wrote:





Elisabeth wrote:

Dear David,

I followed your instructions and calculated Heat of vaporization
of my alkane once with one molecule in gas phase (no cutoff) and
once with equivalent number of molecules as in liquid phase as
Justin suggested. Results are as follows:


To get heat of vaporization, you shouldn't be simulating just a
single molecule in the gas phase, it should be an equivalent number
of molecules as you have in the liquid phase.

Hello David and Justin,

My explanation was not clear. Below is the results for liquid phase
and for gas phase I tried two cases: one single molecule and the other
time for equivalent number of molecules as in liquid phase and thats
why results are very similar. ( However Justin says one single
molecule is not correct. I think when cutoffs is set to zero only
bonded terms are


What is not correct is comparing the potential energy of a liquid system
of many molecules with a "gas phase" of a single molecule. Whether or
not that was something you did still is not entirely clear, but to be
very clear, that's what I was saying is incorrect to do. DHvap is based
on conversion of equivalent systems between liquid and gas.


treated and even where there are many particles in gas phase to get


This is incorrect. Cutoffs of zero mean that all nonbonded interactions
are calculated, they are not truncated.


energies per mole of molecules i.e g_energy -nmol XXX must be used so
values should be colse to a single molecules case.. please correct me!
Anyway results for gas phase are close and this is not the issue now).



You shouldn't need -nmol for any of this. Simply take the potential
energy of the two systems (with equivalent numbers of molecules) and
apply the formula I gave you several emails ago.

NOO


1 molecule in the gas phase  -> Epot(g) in your case 59.2 kJ/mol
N molecules in the liquid phase -> Epot(l) (since this is per mole you 
DO need the -nmol option) in you case 34.7 kJ/mol
DHvap = Epot(g) + kBT - Epot(l) = 59.2+2.5-34.7 = 27 kJ/mol which is 
quite close to hexane (28.9 kJ/mol).




-Justin


Liquid phase:

Energy Average Err.Est. RMSD Tot-Drift
---

LJ (SR) -27.3083 0.01 0.296591 -0.0389173 (kJ/mol)
Coulomb (SR) 6.00527 0.0074 0.122878 0.00576827 (kJ/mol)
Coul. recip. 5.59559 0.0032 0.0557413 0.00316957 (kJ/mol)
Potential *34.6779 * 0.025 1.03468 -0.11177 (kJ/mol)
Total Energy 86.4044 0.026 1.44353 -0.112587 (kJ/mol)




*one single molecule in gas phase*


Energy Average Err.Est. RMSD Tot-Drift
---

LJ (SR) -2.24473 0.073 1.292 0.342696 (kJ/mol)
Coulomb (SR) 11.5723 0.55 2.17577 -2.33224 (kJ/mol)
Potential * 59.244 * 0.94 10.9756 6.35631 (kJ/mol)
Total Energy 106.647 1 15.4828 6.78792 (kJ/mol)

*equivalent number of molecules as in liquid* ( large box 20 nm)

Statistics over 101 steps [ 0. through 2000. ps ], 4
data sets
All statistics are over 11 points

Energy Average Err.Est. RMSD Tot-Drift
---

LJ (SR) -2.16367 0.053 0.171542 0.374027 (kJ/mol)
Coulomb (SR) 11.2894 0.23 0.49105 -1.44437 (kJ/mol)
Potential * 63.2369 * 1.1 2.47211 7.69756 (kJ/mol)
Total Energy 114.337 1.1 2.65547 7.72258 (kJ/mol)


Since pbc is set to NO molecules leave the box and I dont know
if this all right. I hope the difference is acceptable...!


For "pbc = no" there is no box.


0- I am going to do the same calculation but for some polymers
solvated in the alkane. For binary system do I need to look at
nonboded terms? and then run a simulation for a single polymer
in vacuum?

Can you please provide me with a recipe for Delta Hvap of the
solute in a solvent?


The method for calculating heat of vaporization is not dependent
upon the contents of the system; it is a fundamental thermodynamic
definition. Heat of vaporization is not something that can be
calculated from a solute in a solvent. You can calculate DHvap for
a particular system, but not some subset of that system.

Thanks Justin. I am interested in the energy required to vaporize
the solute in a particular solvent not the whole DHvap of the
mixture. do you think this can be achieved by calculating nonbonded
energies between solute and solvent? ( defining energy groups ..)




1- If I want to look at nonboded interactions only, do I have to
add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ?


The PME-related terms contain both solute-solvent, solvent-solvent,
and potentially solute-solute terms (depending on the size and
nature of the solute), so trying to interpret this term in some
pairwise fashion is an exercise in futility.

What you mean is when one uses PME interaction energies between
components can not be decomposed? So the energy groups I defined to
extract nonbonded energies are not giving 

Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:





Elisabeth wrote:

Dear David,

I followed your instructions and calculated Heat of vaporization
of my alkane once with one molecule in gas phase (no cutoff) and
once with equivalent number of molecules as in liquid phase as
Justin suggested. Results are as follows:


To get heat of vaporization, you shouldn't be simulating just a
single molecule in the gas phase, it should be an equivalent number
of molecules as you have in the liquid phase.

Hello David and Justin,

My explanation was not clear. Below is the results for liquid phase and 
for gas phase I tried two cases: one single molecule and the other time 
for equivalent number of molecules as in liquid phase and thats why 
results are very similar. ( However Justin says one single molecule is 
not correct. I think when cutoffs is set to zero only bonded terms are 


What is not correct is comparing the potential energy of a liquid system of many 
molecules with a "gas phase" of a single molecule.  Whether or not that was 
something you did still is not entirely clear, but to be very clear, that's what 
I was saying is incorrect to do.  DHvap is based on conversion of equivalent 
systems between liquid and gas.


treated and even where there are many particles in gas phase to get 


This is incorrect.  Cutoffs of zero mean that all nonbonded interactions are 
calculated, they are not truncated.


energies per mole of molecules i.e g_energy -nmol XXX must be used so 
values should be colse to a single molecules case.. please correct me!  
Anyway results for gas phase are close and this is not the issue now).




You shouldn't need -nmol for any of this.  Simply take the potential energy of 
the two systems (with equivalent numbers of molecules) and apply the formula I 
gave you several emails ago.


-Justin


Liquid phase:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-27.3083   0.01   0.296591 -0.0389173  
(kJ/mol)
Coulomb (SR)6.00527 0.0074   0.122878 0.00576827  
(kJ/mol)
Coul. recip.5.59559 0.0032  0.0557413 0.00316957  
(kJ/mol)
Potential   *34.6779  *0.0251.03468   -0.11177  
(kJ/mol)
Total Energy86.4044  0.0261.44353  -0.112587  
(kJ/mol)



 


*one single molecule in gas phase*


Energy  Average   Err.Est.   RMSD  Tot-Drift

---
LJ (SR)-2.24473  0.073  1.292  
0.342696  (kJ/mol)
Coulomb (SR)11.5723   0.552.17577  
-2.33224  (kJ/mol)
Potential  *  59.244 *  0.9410.9756  
 6.35631  (kJ/mol)
Total Energy106.647  115.4828  
 6.78792  (kJ/mol)


*equivalent number of molecules as in liquid* ( large box 20 nm)

Statistics over 101 steps [ 0. through 2000. ps ], 4
data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
LJ (SR)-2.16367  0.053   0.171542  
0.374027  (kJ/mol)
Coulomb (SR)11.2894   0.230.49105  
-1.44437  (kJ/mol)
Potential *  63.2369*1.12.47211  
 7.69756  (kJ/mol)
Total Energy114.3371.12.65547  
 7.72258  (kJ/mol)



 Since pbc is set to NO molecules leave the box and I dont know
if this all right. I hope the difference is acceptable...!


For "pbc = no" there is no box.


0- I am going to do the same calculation but for some polymers
solvated in the alkane. For binary system do I need to look at
nonboded terms? and then run a simulation for a single polymer
in vacuum?

Can you please provide me with a recipe for Delta Hvap of the
solute in a solvent?


The method for calculating heat of vaporization is not dependent
upon the contents of the system; it is a fundamental thermodynamic
definition.  Heat of vaporization is not something that can be
calculated from a solute in a solvent.  You can calculate DHvap for
a particular system, but not some subset of that system.

Thanks Justin. I am interested in the energy required to vaporize
the solute in a particular solvent not the whole DHvap of the
mixture. do you think this can be achieved by calculating nonbonded
energies between solute and solvent? ( defining energy groups ..)

 



1- If I want to look at nonboded interactions on

Re: [gmx-users] Heat of vap

[Elisabeth]

>
> Elisabeth wrote:
>
>> Dear David,
>>
>> I followed your instructions and calculated Heat of vaporization of my
>> alkane once with one molecule in gas phase (no cutoff) and once with
>> equivalent number of molecules as in liquid phase as Justin suggested.
>> Results are as follows:
>>
>>
> To get heat of vaporization, you shouldn't be simulating just a single
> molecule in the gas phase, it should be an equivalent number of molecules as
> you have in the liquid phase.
>
> Hello David and Justin,

My explanation was not clear. Below is the results for liquid phase and for
gas phase I tried two cases: one single molecule and the other time for
equivalent number of molecules as in liquid phase and thats why results are
very similar. ( However Justin says one single molecule is not correct. I
think when cutoffs is set to zero only bonded terms are treated and even
where there are many particles in gas phase to get energies per mole of
molecules i.e g_energy -nmol XXX must be used so values should be colse to a
single molecules case.. please correct me!  Anyway results for gas phase are
close and this is not the issue now).

Liquid phase:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-27.3083   0.01   0.296591 -0.0389173
(kJ/mol)
Coulomb (SR)6.00527 0.0074   0.122878 0.00576827
(kJ/mol)
Coul. recip.5.59559 0.0032  0.0557413 0.00316957
(kJ/mol)
Potential   *34.6779  *0.0251.03468   -0.11177
(kJ/mol)
Total Energy86.4044  0.0261.44353  -0.112587
(kJ/mol)




>  *one single molecule in gas phase*
>>
>>
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>>
>> ---
>> LJ (SR)-2.24473  0.073  1.292   0.342696
>>  (kJ/mol)
>> Coulomb (SR)11.5723   0.552.17577   -2.33224
>>  (kJ/mol)
>> Potential  *  59.244 *  0.9410.97566.35631
>>  (kJ/mol)
>> Total Energy106.647  115.48286.78792
>>  (kJ/mol)
>>
>> *equivalent number of molecules as in liquid* ( large box 20 nm)
>>
>> Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets
>> All statistics are over 11 points
>>
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>>
>> ---
>> LJ (SR)-2.16367  0.053   0.171542   0.374027
>>  (kJ/mol)
>> Coulomb (SR)11.2894   0.230.49105   -1.44437
>>  (kJ/mol)
>> Potential *  63.2369*1.12.472117.69756
>>  (kJ/mol)
>> Total Energy114.3371.12.655477.72258
>>  (kJ/mol)
>>
>>
>>  Since pbc is set to NO molecules leave the box and I dont know if this
>> all right. I hope the difference is acceptable...!
>>
>>
> For "pbc = no" there is no box.
>
>
>  0- I am going to do the same calculation but for some polymers solvated in
>> the alkane. For binary system do I need to look at nonboded terms? and then
>> run a simulation for a single polymer in vacuum?
>>
>> Can you please provide me with a recipe for Delta Hvap of the solute in a
>> solvent?
>>
>>
> The method for calculating heat of vaporization is not dependent upon the
> contents of the system; it is a fundamental thermodynamic definition.  Heat
> of vaporization is not something that can be calculated from a solute in a
> solvent.  You can calculate DHvap for a particular system, but not some
> subset of that system.
>
> Thanks Justin. I am interested in the energy required to vaporize the
> solute in a particular solvent not the whole DHvap of the mixture. do you
> think this can be achieved by calculating nonbonded energies between solute
> and solvent? ( defining energy groups ..)
>


>
>> 1- If I want to look at nonboded interactions only, do I have to add
>>  Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?
>>
>>
> The PME-related terms contain both solute-solvent, solvent-solvent, and
> potentially solute-solute terms (depending on the size and nature of the
> solute), so trying to interpret this term in some pairwise fashion is an
> exercise in futility.
>
> What you mean is when one uses PME interaction energies between components
> can not be decomposed? So the energy groups I defined to extract nonbonded
> energies are not giving correct values? Sofar I have been defining energy
> groups to calculate nonbonded terms between components _A-A A_B... I hope I
> have not been doing thing wrongly!
>

Please help me out!

Thanks,
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Plea

Re: [gmx-users] Heat of vap

[David van der Spoel]

On 2011-04-03 02.15, Elisabeth wrote:

Dear David,

I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:

*one single molecule in gas phase*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.24473  0.073  1.292   0.342696
(kJ/mol)
Coulomb (SR)11.5723   0.552.17577   -2.33224
(kJ/mol)
Potential *  59.244 *  0.9410.97566.35631  (kJ/mol)
Total Energy106.647  115.48286.78792
(kJ/mol)

*equivalent number of molecules as in liquid* ( large box 20 nm)
This is not correct. You need to simulate the liquid in the liquid 
state. Now you have a dilute gas instead, hence the energy difference is 
very small and due to dimers and trimers in the gas phase. Just extract 
Epot from your previous liquid phase calculations.





Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.16367  0.053   0.171542   0.374027
(kJ/mol)
Coulomb (SR)11.2894   0.230.49105   -1.44437
(kJ/mol)
Potential *  63.2369 *1.12.472117.69756  (kJ/mol)
Total Energy114.3371.12.655477.72258
(kJ/mol)


  Since pbc is set to NO molecules leave the box and I dont know if this
all right. I hope the difference is acceptable...!

0- I am going to do the same calculation but for some polymers solvated
in the alkane. For binary system do I need to look at nonboded terms?
and then run a simulation for a single polymer in vacuum?

Can you please provide me with a recipe for Delta Hvap of the solute in
a solvent?


1- If I want to look at nonboded interactions only, do I have to add
Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?


coulombtype =  PME
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.0


ff: OPLSAA


Appreciate your help,
Best,




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:

Dear David,

I followed your instructions and calculated Heat of vaporization of my 
alkane once with one molecule in gas phase (no cutoff) and once with 
equivalent number of molecules as in liquid phase as Justin suggested. 
Results are as follows:




To get heat of vaporization, you shouldn't be simulating just a single molecule 
in the gas phase, it should be an equivalent number of molecules as you have in 
the liquid phase.



*one single molecule in gas phase*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.24473  0.073  1.292   0.342696  
(kJ/mol)
Coulomb (SR)11.5723   0.552.17577   -2.33224  
(kJ/mol)
Potential  *  59.244 *  0.9410.97566.35631  
(kJ/mol)
Total Energy106.647  115.48286.78792  
(kJ/mol)


*equivalent number of molecules as in liquid* ( large box 20 nm)

Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.16367  0.053   0.171542   0.374027  
(kJ/mol)
Coulomb (SR)11.2894   0.230.49105   -1.44437  
(kJ/mol)
Potential *  63.2369*1.12.472117.69756  
(kJ/mol)
Total Energy114.3371.12.655477.72258  
(kJ/mol)



 Since pbc is set to NO molecules leave the box and I dont know if this 
all right. I hope the difference is acceptable...!




For "pbc = no" there is no box.

0- I am going to do the same calculation but for some polymers solvated 
in the alkane. For binary system do I need to look at nonboded terms? 
and then run a simulation for a single polymer in vacuum?


Can you please provide me with a recipe for Delta Hvap of the solute in 
a solvent?




The method for calculating heat of vaporization is not dependent upon the 
contents of the system; it is a fundamental thermodynamic definition.  Heat of 
vaporization is not something that can be calculated from a solute in a solvent. 
 You can calculate DHvap for a particular system, but not some subset of that 
system.




1- If I want to look at nonboded interactions only, do I have to add  
Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?





The PME-related terms contain both solute-solvent, solvent-solvent, and 
potentially solute-solute terms (depending on the size and nature of the 
solute), so trying to interpret this term in some pairwise fashion is an 
exercise in futility.


-Justin

coulombtype =  PME  
vdw-type=  Shift   
rcoulomb-switch =  0  
rvdw-switch =  0.9
rlist   =  1.2   
rcoulomb=  1.2
rvdw=  1.0   



ff: OPLSAA


Appreciate your help,
Best,



--


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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[gmx-users] Heat of vap

[Elisabeth]

Dear David,

I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:

*one single molecule in gas phase*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.24473  0.073  1.292   0.342696
(kJ/mol)
Coulomb (SR)11.5723   0.552.17577   -2.33224
(kJ/mol)
Potential  *  59.244 *  0.9410.97566.35631
(kJ/mol)
Total Energy106.647  115.48286.78792
(kJ/mol)

*equivalent number of molecules as in liquid* ( large box 20 nm)

Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.16367  0.053   0.171542   0.374027
(kJ/mol)
Coulomb (SR)11.2894   0.230.49105   -1.44437
(kJ/mol)
Potential *  63.2369*1.12.472117.69756
(kJ/mol)
Total Energy114.3371.12.655477.72258
(kJ/mol)


 Since pbc is set to NO molecules leave the box and I dont know if this all
right. I hope the difference is acceptable...!

0- I am going to do the same calculation but for some polymers solvated in
the alkane. For binary system do I need to look at nonboded terms? and then
run a simulation for a single polymer in vacuum?

Can you please provide me with a recipe for Delta Hvap of the solute in a
solvent?


1- If I want to look at nonboded interactions only, do I have to add  Coul.
recip.  to [ LJ (SR)  + Coulomb (SR) ] ?


coulombtype =  PME
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.0


ff: OPLSAA


Appreciate your help,
Best,
-- 
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Please search the archive at 
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Re: [gmx-users] Heat of vap

[David van der Spoel]

On 2011-03-31 19.11, Elisabeth wrote:



On 31 March 2011 12:58, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Elisabeth wrote:



in your mail:


On 30 March 2011 15:30, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:



Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure
alkane system/.  Here is the steps I am taking. Please
correct me.

1- Obtain total energy of system (kinetic+potential) and
divide
by number of molecules to obtain energy per mol of
molecules.
g_energy -f *.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size
as in 1
or it does not matter? (step 1 is done for the actual
denstiy)


More troubling, how does one define the energy of a
molecule?  If
you use any sort of long-range algorithms (especially PME,
but also
dispersion correction), you can't simply decompose the
system like this.

Thanks Justin and David.

I have been trying to find the article in which this has been
presented. If you have time Please see page 5937, right column,
equation 11. I think I made a mistake and I dont have to include
kinetic energy, Only nonboded energies!?

http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539


What is cohesive energy and how does it relate to the quantity
you're trying to calculate?

It is delta Hvap/volume. It is directly related to Hvap. What is
happening is that they are calculating nonbonded energy of some
chains, divide by number of chains and substract from nonbonded
energy of a single chain in vacuum. These are the steps I wrote in
my first post but I think I should not have included kinetic and
should just look at LJ-SR and Coulomb-SR.


I am using PME..If I remember correctly LR is included in Coulomb-SR and
can not get decomposed? But I dont think this doesnt matter since if I
am to take nonbonded energies this should not hurt,,,

Please comment ...

It is simple.
Compute Epot with all normal liquid options (PME, Dispcorr etc.).
Compute Epot for a gas phase molecule without any cutoffs
Apply equation below.
For OPLS/AA we obtain close to 98% correlation between experiment and 
simulation (paper submitted).



In the derivation of recent Gromos96 parameter sets, the heat of
vaporization is quite simple:

DHvap =  -  + RT


1- So  is the total energy or only potential (no kinetic)


Potential.


2- How can I compute ? I have liquid now...


Run a simulation in the gas phase.


Sorry, but how can I do this? :( I have box of molecules with density of
actual liquid..How can I shift to gas phase ..I mean how many molecules
I need to keep in the box..

Many thanks...


-Justin


Thank you,
Regards,


-- 

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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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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Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:



On 31 March 2011 12:58, Justin A. Lemkul > wrote:




Elisabeth wrote:



in your mail:


On 30 March 2011 15:30, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:



   Elisabeth wrote:

   Dear all,

   I intend to obtain vaporization heat per volume for a /pure
   alkane system/.  Here is the steps I am taking. Please
correct me.

   1- Obtain total energy of system (kinetic+potential) and
divide
   by number of molecules to obtain energy per mol of molecules.
   g_energy -f *.edr -nmol XXX
   2- Obtain total energy of a single molecule (use pbc).
   3- Subtract step 2 from step 1.
   4- Divide by simulation box volume.

   My questions is:

   in step 2 : what should be the box size? The same size as
in 1
   or it does not matter? (step 1 is done for the actual
denstiy)


   More troubling, how does one define the energy of a molecule?  If
   you use any sort of long-range algorithms (especially PME,
but also
   dispersion correction), you can't simply decompose the system
like this.

Thanks Justin and David.

I have been trying to find the article in which this has been
presented. If you have time Please see page 5937, right column,
equation 11. I think I made a mistake and I dont have to include
kinetic energy, Only nonboded energies!?

http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539


What is cohesive energy and how does it relate to the quantity
you're trying to calculate?

It is delta Hvap/volume. It is directly related to Hvap. What is
happening is that they are calculating nonbonded energy of some
chains, divide by number of chains and substract from nonbonded
energy of a single chain in vacuum. These are the steps I wrote in
my first post but I think I should not have included kinetic and
should just look at LJ-SR and Coulomb-SR.


I am using PME..If I remember correctly LR is included in Coulomb-SR and 
can not get decomposed? But I dont think this doesnt matter since if I 
am to take nonbonded energies this should not hurt,,,


Please comment ...



PME energies are from nonbonded interactions.  The mesh energy is written to the 
"Coul-recip" term in the .edr file.  If there is some other "Coul (LR)" term, it 
is because you're using a twin-range cutoff such that rcoulomb > rlist, which I 
do not believe is correct when using PME.


 

 
   In the derivation of recent Gromos96 parameter sets, the heat of

   vaporization is quite simple:

   DHvap =  -  + RT


1- So   is the total energy or only potential (no kinetic)


Potential.


2- How can I compute ? I have liquid now...


Run a simulation in the gas phase.


Sorry, but how can I do this? :( I have box of molecules with density of 
actual liquid..How can I shift to gas phase ..I mean how many molecules 
I need to keep in the box..




Make a box with an equivalent number of molecules separated by some large amount 
of space (i.e. 50 nm or so).  Set pbc=no and all cutoffs to zero.  I'm basing 
this on Gromos96 parameterization, but I don't know what your target force field is.


-Justin


Many thanks...


-Justin


   Thank you,
   Regards,


   -- 

   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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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksb

Re: [gmx-users] Heat of vap

[Elisabeth]

On 31 March 2011 12:58, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>>
>>
>> in your mail:
>>
>>
>> On 30 March 2011 15:30, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Elisabeth wrote:
>>
>>Dear all,
>>
>>I intend to obtain vaporization heat per volume for a /pure
>>alkane system/.  Here is the steps I am taking. Please correct me.
>>
>>1- Obtain total energy of system (kinetic+potential) and divide
>>by number of molecules to obtain energy per mol of molecules.
>>g_energy -f *.edr -nmol XXX
>>2- Obtain total energy of a single molecule (use pbc).
>>3- Subtract step 2 from step 1.
>>4- Divide by simulation box volume.
>>
>>My questions is:
>>
>>in step 2 : what should be the box size? The same size as in 1
>>or it does not matter? (step 1 is done for the actual denstiy)
>>
>>
>>More troubling, how does one define the energy of a molecule?  If
>>you use any sort of long-range algorithms (especially PME, but also
>>dispersion correction), you can't simply decompose the system like
>> this.
>>
>> Thanks Justin and David.
>>
>> I have been trying to find the article in which this has been presented.
>> If you have time Please see page 5937, right column, equation 11. I think I
>> made a mistake and I dont have to include kinetic energy, Only nonboded
>> energies!?
>>
>> http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539
>>
>>
> What is cohesive energy and how does it relate to the quantity you're
> trying to calculate?
>
> It is delta Hvap/volume. It is directly related to Hvap. What is happening
> is that they are calculating nonbonded energy of some chains, divide by
> number of chains and substract from nonbonded energy of a single chain in
> vacuum. These are the steps I wrote in my first post but I think I should
> not have included kinetic and should just look at LJ-SR and Coulomb-SR.
>

I am using PME..If I remember correctly LR is included in Coulomb-SR and can
not get decomposed? But I dont think this doesnt matter since if I am to
take nonbonded energies this should not hurt,,,

Please comment ...



>
>>In the derivation of recent Gromos96 parameter sets, the heat of
>>vaporization is quite simple:
>>
>>DHvap =  -  + RT
>>
>>
>> 1- So   is the total energy or only potential (no kinetic)
>>
>
> Potential.
>
>
>  2- How can I compute ? I have liquid now...
>>
>>
> Run a simulation in the gas phase.
>

Sorry, but how can I do this? :( I have box of molecules with density of
actual liquid..How can I shift to gas phase ..I mean how many molecules I
need to keep in the box..

Many thanks...

>
> -Justin
>
>
>>Thank you,
>>Regards,
>>
>>
>>-- 
>>
>>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
>>
>>
>>
>>-- 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
>>
>>
>>
> --
> 
>
> 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
>
> 
> --
> 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
>
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Re: [gmx-users] Heat of vap

[David van der Spoel]

On 2011-03-31 18.52, Elisabeth wrote:



in your mail:

On 30 March 2011 15:30, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure
alkane system/.  Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide
by number of molecules to obtain energy per mol of molecules.
g_energy -f *.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1
or it does not matter? (step 1 is done for the actual denstiy)


More troubling, how does one define the energy of a molecule?  If
you use any sort of long-range algorithms (especially PME, but also
dispersion correction), you can't simply decompose the system like this.

Thanks Justin and David.

I have been trying to find the article in which this has been presented.
If you have time Please see page 5937, right column, equation 11. I
think I made a mistake and I dont have to include kinetic energy, Only
nonboded energies!?
Either Epot or Etot. It does not matter if you simulate at the same 
Temp. You could also consider using the enthalphy (gmx 4.5 and higher).


http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539

In the derivation of recent Gromos96 parameter sets, the heat of
vaporization is quite simple:

DHvap =  -  + RT


1- So  is the total energy or only potential (no kinetic)
2- How can I compute ? I have liquid now...


Thank you,
Regards,


--


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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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:



in your mail:

On 30 March 2011 15:30, Justin A. Lemkul > wrote:




Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure
alkane system/.  Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide
by number of molecules to obtain energy per mol of molecules.
g_energy -f *.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1
or it does not matter? (step 1 is done for the actual denstiy)


More troubling, how does one define the energy of a molecule?  If
you use any sort of long-range algorithms (especially PME, but also
dispersion correction), you can't simply decompose the system like this.

Thanks Justin and David.

I have been trying to find the article in which this has been presented. 
If you have time Please see page 5937, right column, equation 11. I 
think I made a mistake and I dont have to include kinetic energy, Only 
nonboded energies!?


http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539



What is cohesive energy and how does it relate to the quantity you're trying to 
calculate?


 


In the derivation of recent Gromos96 parameter sets, the heat of
vaporization is quite simple:

DHvap =  -  + RT


1- So   is the total energy or only potential (no kinetic)


Potential.


2- How can I compute ? I have liquid now...



Run a simulation in the gas phase.

-Justin



Thank you,
Regards,


-- 



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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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--


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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Re: [gmx-users] Heat of vap

[Elisabeth]

in your mail:

On 30 March 2011 15:30, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>> Dear all,
>>
>> I intend to obtain vaporization heat per volume for a /pure alkane
>> system/.  Here is the steps I am taking. Please correct me.
>>
>> 1- Obtain total energy of system (kinetic+potential) and divide by number
>> of molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol
>> XXX
>> 2- Obtain total energy of a single molecule (use pbc).
>> 3- Subtract step 2 from step 1.
>> 4- Divide by simulation box volume.
>>
>> My questions is:
>>
>> in step 2 : what should be the box size? The same size as in 1 or it does
>> not matter? (step 1 is done for the actual denstiy)
>>
>>
> More troubling, how does one define the energy of a molecule?  If you use
> any sort of long-range algorithms (especially PME, but also dispersion
> correction), you can't simply decompose the system like this.
>
> Thanks Justin and David.

I have been trying to find the article in which this has been presented. If
you have time Please see page 5937, right column, equation 11. I think I
made a mistake and I dont have to include kinetic energy, Only nonboded
energies!?

http://pubs.acs.org/doi/pdfplus/10.1021/jp0707539



> In the derivation of recent Gromos96 parameter sets, the heat of
> vaporization is quite simple:
>
> DHvap =  -  + RT
>

1- So   is the total energy or only potential (no kinetic)
2- How can I compute ? I have liquid now...

>
>  Thank you,
>> Regards,
>>
>>
> --
> 
>
> 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
>
> 
>
> --
> 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
>
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Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure alkane 
system/.  Here is the steps I am taking. Please correct me.


1- Obtain total energy of system (kinetic+potential) and divide by 
number of molecules to obtain energy per mol of molecules. g_energy -f 
*.edr -nmol XXX

2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it 
does not matter? (step 1 is done for the actual denstiy)




More troubling, how does one define the energy of a molecule?  If you use any 
sort of long-range algorithms (especially PME, but also dispersion correction), 
you can't simply decompose the system like this.


In the derivation of recent Gromos96 parameter sets, the heat of vaporization is 
quite simple:


DHvap =  -  + RT

I have seen this equation used in a number of other studies, as well.

-Justin


Thanking you all,
Regards,



--


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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Re: [gmx-users] Heat of vap

[David van der Spoel]

On 2011-03-30 21.22, Elisabeth wrote:

Dear all,

I intend to obtain vaporization heat per volume for a /pure alkane
system/.  Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -f
*.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it
does not matter? (step 1 is done for the actual denstiy)

do turn off all pbc and cutoff for that one.


Thanking you all,
Regards,




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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[gmx-users] Heat of vap

[Elisabeth]

Dear all,

I intend to obtain vaporization heat per volume for a *pure alkane system*.
Here is the steps I am taking. Please correct me.

1- Obtain total energy of system (kinetic+potential) and divide by number of
molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.

My questions is:

in step 2 : what should be the box size? The same size as in 1 or it does
not matter? (step 1 is done for the actual denstiy)

Thanking you all,
Regards,
-- 
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!
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