[gmx-users] calculation of density for martini coarse-grained
mohammad agha
mra_bu at yahoo.com
Thu Dec 15 16:55:58 CET 2011
thanks for your reply.
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
>
>--
>gmx-users mailing list gmx-users at gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>Please don't post (un)subscribe requests to the list. Use
the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111215/8c588c93/attachment.html>
More information about the gromacs.org_gmx-users
mailing list