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

mohammad agha mra_bu at yahoo.com
Thu Dec 15 18:50:02 CET 2011


Dear Prof.

Thank you very much.

Excuse me, I am beginner in gromacs and my experience about warnings is low, but I think my problem return to this warning:
WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

I checked mailing list but I didn't find my answer!
Please help me.

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 6:31 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 

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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