[gmx-users] calculation of density for martini coarse-grained
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Dec 16 09:06:10 CET 2011
Hi Sara,
For calculation of the density you need the masses. Neither editconf
nor genbox uses real masses. They approximate the mass based on a list
of atom names and associated masses, which is quite crude and fails if
the atoms are not listed. Martini beads are not listed...
To get the density you have to look at the .edr file that is written
during the simulation.
Cheers,
Tsjerk
On Fri, Dec 16, 2011 at 7:02 AM, mohammad agha <mra_bu at yahoo.com> wrote:
> Excuse me, I did all of examples in my system with different molecules (even
> water alone) and with different force fields and I took this warning for all
> of them by doing genbox command!!!
>
> 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.
>
> Is this warning for all in this command, always? If not, then why have I
> that always? My density is calculated wrong in gromacs and density is
> important for me!
> Please help me.
>
> Best Regards
> Sara
> ________________________________
> From: mohammad agha <mra_bu at yahoo.com>
> To: "jalemkul at vt.edu" <jalemkul at vt.edu>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Sent: Thursday, December 15, 2011 10:28 PM
>
> Subject: Re: [gmx-users] calculation of density for martini coarse-grained
>
> Thank you very much.
>
> Best Regards
>
> Sara
>
> ________________________________
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, December 15, 2011 10:02 PM
> Subject: Re: [gmx-users] calculation of density for martini coarse-grained
>
>
>
> mohammad agha wrote:
>> Thank you very much for your reply.
>>
>> I experienced "genbox" for gromos force field for my molecules and for
>> dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same
>> warning for all them!!!
>> May I know that what should I do, Please ?
>>
>
> Probably nothing. If you use a coordinate file as input into a number of
> tools you'll likely get the same. As I said, it is a warning, not an error
> that needs fixing. It is up to you, as the user, to verify that the output
> of the program is what you want it to be. Issues related to measured
> density as you've been reporting are likely a consequence of bizarre atom
> names that Gromacs doesn't understand. You have to (correctly) do the math
> to find what the density should be.
>
> -Justin
>
>> Best Regards
>> Sara
>> ------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu>
>> *To:* mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> *Sent:* Thursday, December 15, 2011 9:26 PM
>> *Subject:* Re: [gmx-users] calculation of density for martini
>> coarse-grained
>>
>>
>>
>> mohammad agha wrote:
>> > 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.
>> >
>>
>> The warning indicates that names may give misleading values for masses and
>> van der Waals interactions. For instance, is "CA" an alpha-carbon, or
>> calcium? In this context, the program reporting the error doesn't know.
>> Since MARTINI uses lots of weird atom names for its structures, the program
>> is warning you that the output may be incorrect, or perhaps it may not;
>> hence why it is a warning and not an error.
>>
>> -Justin
>>
>> > 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
>> <mailto:Mark.Abraham at anu.edu.au>>
>> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto: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
>> <mailto:Mark.Abraham at anu.edu.au>> <mailto:Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>>
>> >> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
>> <mailto: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
>> >>
>> >> -- gmx-users mailing list gmx-users at gromacs.org
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>> >>
>> >
>> >
>> > -- gmx-users mailing list gmx-users at gromacs.org
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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