Hi everybody

I’m going to simulate a hydrocarbon system using GROMOS force field. In my work, *Real* was chosen for system unit. In original papers of that paper, bond parameters (K0) are in 10^6 kJ/mol.nm4 and number sounds sensible.

However, when I convert those to corresponding values in *Real* unit, I’ll obtain very small numbers as small as 10^-10! I can’t find such small values in LAMMPS manual.

Could anybody tell me, am I right?

If so, how to include them in the LAMMPS data file to avoid the risk of round-off error in calculation?

Any hint is welcome.

I would double check the correctness of your unit conversion and/or your understanding of the GROMOS units.

Also, please check this out regarding the round-off errors:

https://en.wikipedia.org/wiki/Floating-point_arithmetic

Hi everybody

I'm going to simulate a hydrocarbon system using GROMOS force field. In my

work, *Real* was chosen for system unit. In original papers of that paper,

bond parameters (K0) are in 10^6 kJ/mol.nm4 and number sounds sensible.

However, when I convert those to corresponding values in *Real* unit, I'll

obtain very small numbers as small as 10^-10! I can't find such small

values in LAMMPS manual.

Could anybody tell me, am I right?

this sounds wrong. your conversion doesn't make sense. you should get

numbers in the 10^2 kcal/mol range.

axel.

Thanks Axel

I’ve attached the original paper of GROMOS. Please take a look at table 2, where in the header the bond-stretching constant is 10^6 kJ/mol.nm^4.

So, I convert that unit to Real as follows:

(10^-6)*(1 kcal/4.184kJ)(1 nm/ 10 Ang)^4 ==> (10^-6)(1/4.184)(1/10)^4

I think my calculation is right. But, like you, it sounds wrong!

But, What’s the reason?

A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation The GROMOS Force-Field Parameter Sets 53A5 and 53A6, 2004 .pdf (404 KB)

Thanks Axel

I've attached the original paper of GROMOS. Please take a look at table 2,

where in the header the bond-stretching constant is 10^6 kJ/mol.nm^4.

So, I convert that unit to Real as follows:

(10^-6)*(1 kcal/4.184kJ)(1 nm/ 10 Ang)^4 ==> (10^-6)(1/4.184)(1/10)^4

I think my calculation is right. But, like you, it sounds wrong!

But, What's the reason?

you copied the paper wrong. it is 10^6 *NOT* 10^-6

axel.

OK!

Seemingly, the paper notation has been wrong!

As far as I know, when a number is so small, the authors make use of such notation to reduce decimal

numbers.

Am I right Axel?

OK!

Seemingly, the paper notation has been wrong!

the notation in the paper makes sense and seems correct to me.

axel.