[gmx-users] calculation of density for martini coarse-grained

[Mark Abraham]

On 15/12/2011 5:59 PM, mohammad agha wrote:
> Dear Prof.
>
> May I ask you two questions, Please?
> 1- I work with MARTINI force field. I have a surfactant molecule 
> consists of 5 beads. After I placed 151 surfactants into my simulation 
> box (cubic) with length of 10 nm, Gromacs reported:
>
> Volume = 1000 nm3
> Density = 15.8111 gr/l
>
> My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 = 1000*10e-24 L, 
> but about density, I think that I am wrong:
> 151 * 5 = 755 beads ( since all particle masses are set to 72 amu in 
> MARTINI ), then 755 * 72 amu = 54360 amu,
> and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr
> then, density = 52.23 gr/l but the Gromacs gave 15.8111 gr/l!!!

Please use standard abbreviations for your units unless you want risk 
people not taking you seriously...

I've no idea how you can divide 90254.026*10e-24 by 1000*10e-24 and get 
52.23 or 15.8111

> And there is the same problem after adding water and ion!
> May I know my mistake, Please?
>
> 2- My surfactant molecule has one positive charge, after I added 151 
> surfactants, water and antifreezewater, Gromacs answer me that (for 
> each step):
> NOTE1: system has non-zero total charge: 1.510000e+2
> Then I added 151 ions to my system with -nn 151 for neutralization, 
> but in the genion.log was reported that "System total charge: 151.000"!!!,

When did genion report that, before or after adding ions? Did the 
addition succeed? Are your solvent molecules named "SOL"?

> but after doing grompp, GROMACS didn't report "note" about system 
> charge. Is this right?

We don't know. Copied and pasted command lines and terminal output are a 
lot more useful for getting help than sentences describing them.

Mark
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