[gmx-users] Electrostatic interactions and atoms with nul charge
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Jun 5 11:16:39 CEST 2012
On 5/06/2012 6:46 PM, Laurence Leherte wrote:
> Hello,
>
> Thank you very much for your reply. I actually carried out very basic
> MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw
> = "infinity", niter = 10^6). The computing results are given in the
> two tables below. As they are identical, I am assuming that there is
> only one neighbor list that is created for the calculation of both the
> electrostatic and vdW interactions.
Those settings trigger a different kind of non-bonded kernel from ones
normally used in explicit solvent calculations. These kernels apparently
don't bother to construct Q-only or LJ-only versions. It's probably not
worthwhile for only a handful of atoms in the whole system.
> Since I want to calculate all vdW terms, I suppose that all Coulomb
> terms are automatically calculated too. Am I right ?
>
>
> What if I create a group with all the nul-charge atoms and, by some
> means (e.g., a different fudgeQQ value - or something else- for that
> group ???), avoid to compute the electrostatic interactions with all
> the other charges particules ?
>
>
> Similarly to the problem I reported in my mail, I also want to add
> some kind of charged virtual sites. In that case, those sites should
> not contribute to the vdW interactions of the system. I found no
> problem at all to define such virtual sites and to carry out MD
> simulations, but I suspect vdW terms to be calculated even if epsilon
> and sigma are set equal to zero for such "particles".
Yes, but the whole thing is so cheap it's not worth thinking about.
Mark
> Thank you in advance for any help
>
> Laurence
>
>
>
> For the regular MD (all atoms bear a non-zero charge) :
> Computing: M-Number M-Flops % Flops
> -----------------------------------------------------------------------------
> All-vs-All, Coul + LJ 19404.019404 737352.737 72.1
> Outer nonbonded loop 197.000197 1970.002 0.2
> 1,4 nonbonded interactions 518.000518 46620.047 4.6
> Bonds 105.000105 6195.006 0.6
> Angles 363.000363 60984.061 6.0
> Propers 674.000674 154346.154 15.1
> Virial 24.200242 435.604 0.0
> Stop-CM 19.700197 197.002 0.0
> Calc-Ekin 197.000394 5319.011 0.5
> Lincs 96.000288 5760.017 0.6
> Lincs-Mat 468.001404 1872.006 0.2
> Constraint-V 192.000384 1536.003 0.2
> Constraint-Vir 9.600096 230.402 0.0
> -----------------------------------------------------------------------------
> Total 1022818.053 100.0
>
>
> For the modified system (most of the atoms, i.e. 169 over 197, bear a
> nul charge) :
> Computing: M-Number M-Flops % Flops
> -----------------------------------------------------------------------------
> All-vs-All, Coul + LJ 19404.019404 737352.737 72.1
> Outer nonbonded loop 197.000197 1970.002 0.2
> 1,4 nonbonded interactions 518.000518 46620.047 4.6
> Bonds 105.000105 6195.006 0.6
> Angles 363.000363 60984.061 6.0
> Propers 674.000674 154346.154 15.1
> Virial 24.200242 435.604 0.0
> Stop-CM 19.700197 197.002 0.0
> Calc-Ekin 197.000394 5319.011 0.5
> Lincs 96.000288 5760.017 0.6
> Lincs-Mat 468.001404 1872.006 0.2
> Constraint-V 192.000384 1536.003 0.2
> Constraint-Vir 9.600096 230.402 0.0
> -----------------------------------------------------------------------------
> Total 1022818.053 100.0
> -----------------------------------------------------------------------------
>
>
>
>
> On 04/06/2012 16:37, Mark Abraham wrote:
>> On 5/06/2012 12:08 AM, Laurence Leherte wrote:
>>> Dear Gromacs users,
>>>
>>> I am using the Amber99 FF in MD simulations of peptides (and
>>> proteins). In a first stage to the design a different charge
>>> distribution, most of the atomic charges were set equal to zero
>>> (i.e., all charges but the C and O backbone atoms).
>>> It appeared that the calculation times observed for the original
>>> all-atom charges and the modified system are similar.
>>>
>>> My question is thus the following one. In order to save calculation
>>> time (and whatever the FF is), how is it possible to avoid that the
>>> atoms bearing a nul charge are considered in electrostatic
>>> calculations ? I should specify here that I want these atoms to be
>>> considered in the vdW non-bonding interactions.
>>
>> IIRC GROMACS neighbour searching already identifies atoms with zero
>> charge and/or LJ parameters and uses non-bonded code that does not
>> compute contributions that are known to be zero. You should be able
>> to see this from the differences in the flop accounting at the end of
>> your .log files when you have different numbers of zero-charge atoms.
>> If the total calculation times are similar, then the number of atoms
>> for which time was saved was negligible. This would be normal for a
>> peptide in a much larger quantity of water. You will have to judge
>> the truth of this from the timing and flop breakdown at the end of
>> the .log file.
>>
>> Mark
>
>
> --
>
>
> Laurence Leherte
> Laboratoire de Physico-Chimie Informatique
> Unité de Chimie Physique Théorique et Structurale
> Facultés Universitaires Notre-Dame de la Paix (University of Namur)
> Rue de Bruxelles, 61
> B-5000 Namur
> Belgique (Belgium)
>
>
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