# [gmx-users] Re: NPT simulation

Sun Aug 29 20:16:16 CEST 2010

```Hello Dr. Chaban,

System size is 5 *5*3 nm when density reaches around 600 SI. Can you please
explain what do you mean by "What about dependence heat of evaporation vs
system size ?". I dont know how to compute vap. heat in gromacs!

Unfortunately, I am still unclear about energy units. :(
Yes, only when I use
g_energy -f ener.edr -o energy.xvg -nmol 8       I get pretty similar values
as you obtained (around 2200 KJ/molecule !? ) but then units should be
energy per molecule. I am confused because Before you had said units are per
mole. Without using -nmol 8 option total energy is around 20,000 (apparently
g_energy by default gives  KJ/mole)

Another reason I am confused is because

g_energy -f ener.edr -o energy.xvg according to manual chapter 2 should give
energies in KJ/mol and not system. I did some simulations for different
number of polymer chains in a big box. (1, 2, 4, 8 chains). The magnitude of
energy values increase as number of chains increase..My question is if
values are in the units of KJ/mol why let's say nonbonded interaction energy
values are increasing in value as number of molecuels goes up? Should not
the values be the same if we are referring to MOLE number of molecules?

I know manual can not be wrong but from what I see it makes more sense if
unit is energy/system!

Thanks,

2010/8/27 Vitaly Chaban <vvchaban at gmail.com>

> Dear Moeed:
>
> 1. Please note, this is Justin here who likes long descriptions but I like
> those which are as short as possible. :-) Please formulate your questions
> more specifically because I am too lazy (and busy unfortunately) to read all
> your MD novels at ones.
>
> 2. If I said that the energy was given per mole, than it is given per mole
> of molecules, not systems, be sure. Use g_energy -nmol  XXX where it is
> reasonable. I think your energy vlue before was correct, just divide it by
> NMOL.
>
> 3. Use NVT (no barostat) if you really need some speficif density.
> Calculate the box size by hand.
>
> 4. Polymers are rather specific MD systems. I think your 1 PE + 343 hexanes
> should be a minimal good composition. By the way, what is the size of MD box
> in nmxnmxnm? What about dependence heat of evaporation vs system size ?
>
> 5. If I am not mistaken "LJ-SR" is a total Lennard-Jones energy of system
> except 1-4 interactions. If I am not true, please somebody correct me.
>
> 6. Just equilibrate the system to avoid volume dances in the production
> run.
>
> Good luck!
>
> --
> Dr. Vitaly V. Chaban
> Department of Chemistry
> University of Rochester,
> Rochester, NY, U.S.A.
>
>
>
> Dear Dr.Chaban,
>
> Thanks for your message.  Now I  have to groups: PE is a single chain and
> HEX (343 hexane molecules). I am interested in nonbonded interaction
> energies between PE and solvent as well as between PE-PE and HEX -HEX. I
> ran
> the simulation for 300ps and the system is equilibrating (300K and 30bar
> and
> also total energy relaxes to a 46000KJ/mol). Actually I can not trust these
> results since if you remember you got much less energy terms.. I was
> shameful of bothering you and discussing about that at that time since I
> thought it does not make sense getting different results with a same
> parameter file and gerometry.  You said it might be because I am getting
> results in a different unit but in fact to get the energy break down I just
> issue g_energy command and dont touch anything. So energy values listed
> below should be in KJ/mol (MOLE by default and not molecule). Since H and C
> are the only atoms present in the system I have switched off electrostatics
> and total energy is about 46000KJ/mol. I would be thankful if you could
> take
> a look at my system in a proper time.
>
>
> - the density I am getting is about 650 SI and I need sth about 400. In
> general the key parameter to change density in NPT is pressure right? so I
> could use P=20bar to get less density and it is kind of try and error . am
> I
> right?
>
> - I have still a foggy image of the system size in simulations. How can I
> decide on number of polymer and solvent particles in system? (of course the
> smaller the better in terms of simulation time..) but the reason I am
> this is because I ran simulations for different number of polymer chains
> (1,2,4,8) and I saw energy terms as total energy increase in value as
> systmes becomes larger. If units are in energy/mol so why is this
> happening?
> It does not make sense to calculate energy for a certain (MOLE) amount of
> molecules and get different  values for different system size. (in brief: I
> can no t decide on number of polymer and hexane molecules)
>
> -now in this system there is only one polymer chain and energy breakdown
> shows energy for PE-PE LJ SR and 1-4. Does it make sanse to have SR within
> a
> single chain? (does this come from 1-5,1-6....interactions on chain? in
> case
> of hexane this can be only 1-5,1-6,1-7 becase there are no more than 7
> bonds
> away each atom) LJ-SR:HEX-HEX    = -7651.06,  & LJ-SR:PE-PE =-96.7831
>
> -at the beginning of the simulation I see the system is decreasing in size
> and after about 10ps box expands again and after 20th ps starts contracting
> again. (volume starts from 8000 nm3 and reaches around 500 then increases
> to
> 1600 nm3 and after that converges nicely to a plateau..). I tried both
> semiisotropic and isotropic options but the same behaviour has been
> observed.
>
>
> I appreciate any help and comment...
> Moeed :)
>
> **********************************************************************
>
> Energy                      Average       RMSD     Fluct.      Drift
> Tot-Drift
>
> -------------------------------------------------------------------------------
> Bond                         8536.6    562.056    441.004    4.02362
> 1207.09
> Angle                       13076.1    682.442    576.028     4.2256
> 1267.69
> Ryckaert-Bell.              3276.27    329.245    302.614   -1.49785
> -449.355
> LJ-14                       1762.95    58.3619    57.9592  0.0790304
> 23.7092
> Coulomb-14                        0          0          0
> 0          0
> LJ (SR)                    -8457.99    2676.83    1915.36   -21.5925
> -6477.77
> Coulomb (SR)                      0          0          0
> 0          0
> Potential                   18193.9    1946.39    1467.66   -14.7621
> -4428.64
> Kinetic En.                 27009.8    325.523     325.51  0.0343522
> 10.3057
> Total Energy                45203.7       1970    1501.36   -14.7277
> -4418.33
> Temperature                 299.914    3.61457    3.61442 0.000381443
> 0.114433
> Pressure (bar)              30.8942    533.069    533.059  0.0378739
> 11.3622
> Box-X                       5.41674    2.51691    2.19253 -0.0142718
> -4.28156
> Box-Y                       5.41674    2.51691    2.19253 -0.0142718
> -4.28156
> Box-Z                       5.02579    2.60455    2.00013 -0.0192635
> -5.77908
> Volume                      306.955    929.783    856.612   -4.17472
> -1252.42
> Density (SI)                530.808    191.837      139.2    1.52423
> 457.271
> #Surf*SurfTen              -3.00385    3396.99    3396.96   0.165929
> 49.779
> Coul-SR:PE-PE                     0          0          0
> 0          0
> LJ-SR:PE-PE                -96.7831    12.0843     11.971  0.0190581
> 5.71744
> Coul-14:PE-PE                     0          0          0
> 0          0
> LJ-14:PE-PE                 145.957    10.2536    10.2529 0.00134961
> 0.404885
> Coul-SR:PE-HEX                    0          0          0
> 0          0
> LJ-SR:PE-HEX               -710.145    226.458    156.934   -1.88519
> -565.559
> Coul-14:PE-HEX                    0          0          0
> 0          0
> LJ-14:PE-HEX                      0          0          0
> 0          0
> Coul-SR:HEX-HEX                   0          0          0
> 0          0
> LJ-SR:HEX-HEX              -7651.06    2451.43    1758.13   -19.7263
> -5917.92
> Coul-14:HEX-HEX                   0          0          0
> 0          0
> LJ-14:HEX-HEX               1616.99    56.0996    55.6947  0.0776808
> 23.3043
>
> *************************************************************************
> pbc              =  xyz                   ; use priodic BCs in all
> directions
> energygrps          =  PE HEX
>
> ;        Run control
> integrator          =  md
> dt                  =  0.001
> nsteps              =  300000
> nstcomm             =  1
>
> ;        Output control
> nstenergy           =  100
> nstxout             =  100
> nstvout             =  0
> nstfout             =  0
> nstlog              =  1000
> nstxtcout          =  0
>
> ;        Neighbor searching
> nstlist             =  10                 ;
> ns_type             =  grid
>
> ;        Electrostatics/VdW
> ;coulombtype         =  PME
> vdw-type            =  Shift
> rcoulomb-switch     =  0
> rvdw-switch         =  0.9
>
> ;        Cut-offs
> rlist               =  1.1
> rcoulomb            =  1.1 ;1.0
> rvdw                =  1.0
>
> ;        Temperature coupling
> Tcoupl              =  v-rescale
> tc-grps             =  System
> tau_t               =  0.1
> ref_t               =  300
>
> ;        Pressure coupling
> Pcoupl              =  Parrinello-Rahman;berendsen
> Pcoupltype          =  semiisotropic    ;isotropic ;
> tau_p               =  1      1
> compressibility     =  4.5e-5 4.5e-5
> ref_p               =  30.0    30.0
>
> ;        Velocity generation
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
> ;        Bonds
> constraints         =  none
> constraint-algorithm = lincs
>
>
>

--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering