<html><body><div style="color:#000; background-color:#fff; 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><br>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><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>_______________________________________________________________________________________________________<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>__________________________________________________________________________________________________<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><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 face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <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>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div> </div> </div></body></html>