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On 15/12/2011 5:59 PM, mohammad agha wrote:
<blockquote
cite="mid:1323932390.96305.YahooMailNeo@web125706.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>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
cite="mid:1323932390.96305.YahooMailNeo@web125706.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;">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
cite="mid:1323932390.96305.YahooMailNeo@web125706.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;"> 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>
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