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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 15 16:01:30 CET 2011


On 16/12/2011 1:36 AM, mohammad agha wrote:
> Dear Prof.
>
> Thank you for your reply.
> I'm really sorry for my mistake in writing the density!! my calculated 
> density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
> In the martini_v2.0.itp file, has been written "all particle masses 
> are set to 72 amu". May I know my mistake, Please?
>
> My solvent molecules aren't named "SOL".
>
> Command lines and terminal outputs:
>
> 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
> output of terminal is:
> Output configuration contains 755 atoms in 151 residues
> Volume                 :        1000 (nm^3)
> Density                :     15.8111 (g/l)
> Number of SOL molecules:      0

One possibility is that the Martini force field doesn't have the masses 
set up correctly for genbox to match from the coordinate file. Perhaps 
in share/top/atommass.dat?

> 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 
> -center 7.4 7.4 7.4
> Output of terminal:
> Read 755 atoms
> Volume: 1000 nm^3, corresponds to roughly 450000 electrons
> No velocities found
>     system size :  9.803  9.897  9.978 (nm)
>     diameter    : 13.969               (nm)
>     center      :  5.239  4.900  4.932 (nm)
>     box vectors : 10.000 10.000 10.000 (nm)
>     box angles  :  90.00  90.00  90.00 (degrees)
>     box volume  :1000.00               (nm^3)
>     shift       :  2.161  2.500  2.468 (nm)
> new center      :  7.400  7.400  7.400 (nm)
> new box vectors : 14.800 14.800 14.800 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  :3241.79               (nm^3)

So the box volume of 2.gro is not 1000 nm^3.

>
> 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
> output of terminal:
> NOTE 1 [file topol.top, line 22]:
>   System has non-zero total charge: 1.510000e+02
>
> 3- mdrun -v -deffnm e1
>
> 4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551
> output of terminal:
> Output configuration contains 33306 atoms in 32702 residues
> Volume                 :     3241.79 (nm^3)
> Density                :     3070.15 (g/l)
> Number of SOL molecules:      0
> _______________________________________________________________________________________________________
> I have a problem about density in step 4 after adding water, again!!!

Could be the same issue - apparently the water is something like three 
times as heavy as normal water (whose density is around 1000g/L).

> _______________________________________________________________________________________________________
> 5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr
> output of terminal:
> NOTE 1 [file topol.top, line 22]:
>   System has non-zero total charge: 1.510000e+02
>
> Analysing residue names:
> There are: 32702      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and 
> splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 99915.00
> This run will generate roughly 49 Mb of data
>
> There was 1 note
>
> 6- mdrun -v -deffnm e3
>
> 7-  genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151
> output of terminal:
> Reading file e3.tpr, VERSION 4.5.4 (single precision)
> Using a coulomb cut-off of 1.2 nm
> Will try to add 0 NA ions and 151 cl- ions.
> Select a continuous group of solvent molecules
> Group     0 (         System) has 33306 elements
> Group     1 (          Other) has 33306 elements
> Group     2 (            CA) has   755 elements
> Group     3 (              W) has 32551 elements
> Select a group: 3
> __________________________________________________________________________________________________
> Adding ions was done successfully but in the genion.log file had been 
> written "System total charge: 151.000"

That would be normal before adding ions, and indicative of a problem 
after adding ions, but you haven't made this clear... You say it was 
successful, and then announce that it reports a total charge consistent 
with failure. If genion succeeded in changing some solute to ions, its 
output is very clear about this.

> __________________________________________________________________________________________________
> 8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1
> output of terminal:
> WARNING 1 [file topol.top, line 23]:
>   151 non-matching atom names
>   atom names from topol.top will be used
>   atom names from 4.gro will be ignored

Don't use -maxwarn unless you can write down why it is OK... fix the 
problem. Apparently one file doesn't have the changes to the ions.

Mark

>
> Analysing residue names:
> There are: 32702      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and 
> splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 99915.00
> This run will generate roughly 49 Mb of data
>
> There was 1 warning
> ____________________________________________________________________________________________________
> My topol.top file is:
> #include "martini_v2.0.itp"
> #include "martini_v2.0_ions.itp"
> #include "martini_v2.0_lipids.itp"
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> [ system ]
> CA in water
>
> [ molecules ]
> CA  151
> W           32400
> cl-         151
> _______________________________________________________________________________________________________
>
> Best Regards
> Sara
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Thursday, December 15, 2011 11:19 AM
> *Subject:* Re: [gmx-users] calculation of density for martini 
> coarse-grained
>
> 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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