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On 2/05/2012 5:37 PM, Mark Abraham wrote:
<blockquote cite="mid:4FA0E43C.1060308@anu.edu.au" type="cite">
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On 2/05/2012 5:12 PM, Anik Sen wrote:
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cite="mid:BDE9D87D31C781498280133FD1BE69A51DE3DF9C@EXCHANGE.csmcri.org"
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<div style="direction:ltr; font-family:Tahoma; color:#000000;
font-size:10pt">Hi,<br>
<font style="font-family:Times New Roman" size="4"> Am
Anik Sen, using gromacs 3.3.2 version. I have a very simple
question to ask, <br>
<br>
In the mdp file, like the emmod.mdp or run.mdp needed for a
MD run there are three factors namely,<span
style="font-weight:bold"> rlist, rcoulomb and rvdw.</span><br>
1. Is there any minimum value for these three below which
the results will be absurd for any system, or we can use any
value for these?<br>
2. For a system we are using 0.1. Is this a right one or
not?</font><br>
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</blockquote>
<font size="4"><br>
You should be attempting to replicate either the parameter
regime under which your force field was developed, or a similar
set under which it has been shown to produce results that agree
with real observations. Pulling numbers out of the air is not
appropriate.</font><br>
</blockquote>
<font size="4"><br>
And since this is apparently new work, you should upgrade to a
more modern GROMACS for much better performance, more useful
resources and hopefully fewer bugs!<br>
<br>
Mark<br>
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