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On 16/12/2011 1:36 AM, mohammad agha wrote:
<blockquote
cite="mid:1323959796.47388.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">
<div><span>Dear Prof.</span></div>
<div><br>
<span></span></div>
<div><span>Thank you for your reply.</span></div>
<div><span>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?</span></div>
<div>In the martini_v2.0.itp file, has been written "all
particle masses are set to 72 amu". May I know my mistake,
Please?</div>
<div><br>
</div>
<div>My solvent molecules aren't named "SOL".</div>
<div><br>
</div>
<div>Command lines and terminal outputs:</div>
<div><br>
</div>
<div>1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro</div>
<div>output of terminal is:</div>
<div>Output configuration contains 755 atoms in 151 residues<br>
Volume : 1000 (nm^3)<br>
Density : 15.8111 (g/l)<br>
Number of SOL molecules: 0 </div>
</div>
</blockquote>
<br>
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?<br>
<br>
<blockquote
cite="mid:1323959796.47388.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">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 <br>
Output of terminal:<br>
Read 755 atoms<br>
Volume: 1000 nm^3, corresponds to roughly 450000 electrons<br>
No velocities found<br>
system size : 9.803 9.897 9.978 (nm)<br>
diameter : 13.969 (nm)<br>
center : 5.239 4.900 4.932 (nm)<br>
box vectors : 10.000 10.000 10.000 (nm)<br>
box angles : 90.00 90.00 90.00 (degrees)<br>
box volume :1000.00 (nm^3)<br>
shift : 2.161 2.500 2.468 (nm)<br>
new center : 7.400 7.400 7.400 (nm)<br>
new box vectors : 14.800 14.800 14.800 (nm)<br>
new box angles : 90.00 90.00 90.00 (degrees)<br>
new box volume :3241.79 (nm^3)<br>
</div>
</blockquote>
<br>
So the box volume of 2.gro is not 1000 nm^3.<br>
<br>
<blockquote
cite="mid:1323959796.47388.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;"><br>
3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr<br>
output of terminal:<br>
NOTE 1 [file topol.top, line 22]:<br>
System has non-zero total charge: 1.510000e+02<br>
<br>
3- mdrun -v -deffnm e1 <br>
<br>
4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 <br>
output of terminal: <br>
Output configuration contains 33306 atoms in 32702 residues<br>
Volume : 3241.79 (nm^3)<br>
Density : 3070.15 (g/l)<br>
Number of SOL molecules: 0 <br>
_______________________________________________________________________________________________________<br>
I have a problem about density in step 4 after adding water,
again!!!<br>
</div>
</blockquote>
<br>
Could be the same issue - apparently the water is something like
three times as heavy as normal water (whose density is around
1000g/L).<br>
<br>
<blockquote
cite="mid:1323959796.47388.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">_______________________________________________________________________________________________________<br>
5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr <br>
output of terminal: <br>
NOTE 1 [file topol.top, line 22]:<br>
System has non-zero total charge: 1.510000e+02<br>
<br>
Analysing residue names:<br>
There are: 32702 Other residues<br>
Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...<br>
Number of degrees of freedom in T-Coupling group rest is
99915.00<br>
This run will generate roughly 49 Mb of data<br>
<br>
There was 1 note<br>
<br>
6- mdrun -v -deffnm e3<br>
<div><br>
</div>
<div>7- genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn
151</div>
<div>output of terminal:</div>
<div>Reading file e3.tpr, VERSION 4.5.4 (single precision)<br>
Using a coulomb cut-off of 1.2 nm<br>
Will try to add 0 NA ions and 151 cl- ions.<br>
Select a continuous group of solvent molecules<br>
Group 0 ( System) has 33306 elements<br>
Group 1 ( Other) has 33306 elements<br>
Group 2 ( CA) has 755 elements<br>
Group 3 ( W) has 32551 elements<br>
Select a group: 3<br>
</div>
<div>__________________________________________________________________________________________________<br>
</div>
<div>Adding ions was done successfully but in the genion.log
file had been written "System total charge: 151.000"<br>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:1323959796.47388.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">
<div>__________________________________________________________________________________________________<br>
</div>
<div>8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr
-maxwarn 1<br>
output of terminal:</div>
<div>WARNING 1 [file topol.top, line 23]:<br>
151 non-matching atom names<br>
atom names from topol.top will be used<br>
atom names from 4.gro will be ignored<br>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1323959796.47388.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:verdana, helvetica, sans-serif;font-size:12pt">
<div><br>
Analysing residue names:<br>
There are: 32702 Other residues<br>
Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...<br>
Number of degrees of freedom in T-Coupling group rest is
99915.00<br>
This run will generate roughly 49 Mb of data<br>
<br>
There was 1 warning<br>
____________________________________________________________________________________________________<br>
</div>
<div>My topol.top file is:</div>
<div>#include "martini_v2.0.itp"<br>
#include "martini_v2.0_ions.itp"<br>
#include "martini_v2.0_lipids.itp"<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
[ system ]<br>
CA in water<br>
<br>
[ molecules ]<br>
CA 151<br>
W 32400<br>
cl- 151<br>
_______________________________________________________________________________________________________<br>
</div>
<div><br>
</div>
<div>Best Regards</div>
Sara
<div style="font-family: verdana, helvetica, sans-serif;
font-size: 12pt;">
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;"> <font size="2" face="Arial">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Thursday, December 15, 2011 11:19 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] calculation of density for martini
coarse-grained<br>
</font> <br>
<div id="yiv729884735">
<div> On 15/12/2011 5:59 PM, mohammad agha wrote:
<blockquote type="cite">
<div style="color:rgb(0, 0,
0);background-color:rgb(255, 255,
255);font-family:verdana, helvetica, sans-serif;
font-size:12pt;">
<div>Dear Prof.</div>
<br>
May I ask you two questions, Please?<br>
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:<br>
<br>
Volume = 1000 nm3<br>
Density = 15.8111 gr/l<br>
<br>
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:<br>
151 * 5 = 755 beads ( since all particle masses are
set to 72 amu in MARTINI ), then 755 * 72 amu =
54360 amu,<br>
and 54360 amu / 6.023*10e+23 = 90254.026*10e-24 gr<br>
then, density = 52.23 gr/l but the Gromacs gave
15.8111 gr/l!!!<br>
</div>
</blockquote>
<br>
Please use standard abbreviations for your units unless
you want risk people not taking you seriously...<br>
<br>
I've no idea how you can divide 90254.026*10e-24 by
1000*10e-24 and get 52.23 or 15.8111<br>
<br>
<blockquote type="cite">
<div style="color:rgb(0, 0,
0);background-color:rgb(255, 255,
255);font-family:verdana, helvetica, sans-serif;
font-size:12pt;">And there is the same problem after
adding water and ion!<br>
May I know my mistake, Please?<br>
<br>
2- My surfactant molecule has one positive charge,
after I added 151 surfactants, water and
antifreezewater, Gromacs answer me that (for each
step):<br>
NOTE1: system has non-zero total charge: 1.510000e+2<br>
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"!!!,</div>
</blockquote>
<br>
When did genion report that, before or after adding
ions? Did the addition succeed? Are your solvent
molecules named "SOL"?<br>
<br>
<blockquote type="cite">
<div style="color:rgb(0, 0,
0);background-color:rgb(255, 255,
255);font-family:verdana, helvetica, sans-serif;
font-size:12pt;"> but after doing grompp, GROMACS
didn't report "note" about system charge. Is this
right? <br>
</div>
</blockquote>
<br>
We don't know. Copied and pasted command lines and
terminal output are a lot more useful for getting help
than sentences describing them.<br>
<br>
Mark<br>
</div>
</div>
<br>
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