I checked mailing list but I didn't find my answer!
Please help me.
Best Regards
Sara
------------------------------------------------------------------------
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
<mailto:gmx-users@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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