[gmx-users] To know

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 2 09:44:37 CEST 2012

On 2/05/2012 5:37 PM, Mark Abraham wrote:
> On 2/05/2012 5:12 PM, Anik Sen wrote:
>> Hi,
>>       Am Anik Sen, using gromacs 3.3.2 version. I have a very simple 
>> question to ask,
>> In the mdp file, like the emmod.mdp or run.mdp needed for a MD run 
>> there are three factors namely,rlist, rcoulomb and rvdw.
>> 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?
>> 2. For a system we are using 0.1. Is this a right one or not?
> 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.

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!

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