[gmx-users] Treating nonbondend interactions in GROMACS

Sun Jul 11 01:53:12 CEST 2010

Hello Justin,

Thanks for your comments and also I really liked your reasoning for getting
no answer from people that are not awake :)))) You are right ;)

Actually, I have no charged particles in my system. All I have is carbon and
hydrogen. I read through the manual meticulously about nonbonded interaction
terms. I would like you to correct me if I am wrong. See the summary below
(my understanding) please:

Treating nonbonded interactions for a hydrocarbon system:

1-Short range:

vdw: shift
electrostatics: shift

so the settings would be :
rvdw=1
rcoulomb=1
rlist=1.1
rcoulomb-switch=0
(when this is zero means shift function is added to actual function for all
r?)

I have a question here: in manual I read setting this last parameter nonzero
means it acts as a switch function. I thought if it is nonzero shift acts
just at a nonzero-r between zero and r_c (rcoulomb or rvdw)

2-Long range

vdw: Dispcorr:Enerpres
electrostatics: PME

There are 2 issues from last post (quotes) I am unsure about.

"in md.mdp file I have only coulombtype=PME"

"This contradicts your statement above.  You said you had only uncharged
particles, but clearly this is not the case."

What you mean is Basically that I dont need to consider PME for hydrocarbon
system?

and if you mean I am using wrong setting:

I do not know how else I can treat LR electrostatics in my system. I read in
the manual that PME almost for all cases performs better than Ewald and also
PPPM cant do P coupling so I picked PME :)

Also you said:
"A method like PME is significantly more accurate, but you can also achieve
reasonable results using switch, shift, etc.  Read about the relevant
mechanics of the force field you're using for what might be appropriate."

>From what your statement above I realize that PME and shift or switch func's
are different alternatives. To be honest I am a little confused about the
methods for treating nonbonded interactions. Thats why I wrote that little
summary above so that you can correct me. This could be useful for other
beginners as well. My understanding from reading the manual is that PME is
for LR and switch and shift functions for SR. How could they be
alternatives?

Thank you,

On 9 July 2010 20:15, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> jojo J wrote:
>
>> Dear experts,
>>
>> I posted this message before but I think you did not see it since I
>> noticed messages after this have been replied. I have a hydrocarbon
>>
>
> Messages do not receive replies in any sort of order.  Probably no one has
> had any relevant comments yet, or they live in a time zone where they are
> not awake :)
>
>
>  system with no charged particles. Today In one of the GROMACS tutorials I
>> saw the following setting in em.mdp file:
>> fourierspacing      =  0.12
>> ;fourier_nx          =   0
>> ;fourier_ny          =   0
>> ;fourier_nz          =   0
>> ;pme_order          =   4
>> ;ewald_rtol         =  1e-5
>> ;optimize_fft      =  yes
>>
>> has been used for PME . Sofar I did not even include coulombtype=PME in my
>> em.mdp file. What I had was:
>> constraints         =  all-bonds
>> integrator          =  steep
>> dt                  =  0.002    ; ps !
>> nsteps              =  200
>> nstlist             =  10
>> ns_type             =  grid
>> rlist               =  1.0
>> rcoulomb            =  1.0
>> rvdw                =  1.0
>> ;
>> ;       Energy minimizing stuff
>> ;
>> emtol               =  1000.0
>>
>> Can you please guide me whether it is necessary to include these lines in
>> em file for system having only partial charges like hydrocarbon (alkane).
>> Also, in md.mdp file I have only coulombtype=PME and not the
>>
>
> This contradicts your statement above.  You said you had only uncharged
> particles, but clearly this is not the case.
>
>
>  above Ewald settings. Do you recommend to include those settings?
>>
>
> For energy minimization, the effects of plain cutoffs may or may not be
> significant.  Using plain cutoffs for actual simulation is a bad idea.  The
> artifacts are well-documented and for modern simulations any good reviewer
> should raise an immediate concern if plain cutoffs were used and not
> thoroughly justified.  A method like PME is significantly more accurate, but
> you can also achieve reasonable results using switch, shift, etc.  Read
> about the relevant mechanics of the force field you're using for what might
> be appropriate.
>
>
>  Without the mentioned lines I am getting reasonabel results (potential
>> energy, kinetic, ,, also T coupling works perfectly). If I had better to
>> unclude them what is the best value for fourierspacing?
>>
>>
> I don't think there's ever been any sort of systematic study on the effects
> of Fourier grid spacing.  The trade-off is between speed and accuracy.
>  Larger values speed up calculations, but make PME less accurate.  Smaller
> values have the opposite effect.  You could do a small test for yourself
> (0.12, 0.16, 0.18...) to see if there are any adverse effects.
>
> -Justin
>
>  Thank you,
>>
>>
> --
> ========================================
>
> 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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