[gmx-users] Electrostatic interactions and atoms with nul charge

[Laurence Leherte]

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.  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".

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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