[gmx-users] Re: Constraints - PMF - Different Molecules

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 17 16:04:07 CET 2008

Eudes Fileti wrote:
>>  The error you report is potentially of the everyday
>> http://wiki.gromacs.org/index.php/blowing_up variety. See
>> http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
>> First, get your separated-molecules topology and initial structure
>> working for basic MD. Then combine the topologies. Only then introduce
>> your next layer of complexity with constraints-restraints. Then worry
>> about PMF stuff. Even for experts, troubleshooting where something went
>> wrong is easier if you only make one lot of changes at a time before
>> testing for correctness.

 > Hi Mark, sorry, but could you be more specific when
 > you say "Combine the topologies"?
 > Was not it what I had done early?

Indeed, you had done something very close to a successful combination, 
and I did not see a problem with it. However your subsequent 
observations could have been caused by all manner of problems, including 
a bad initial structure. Such a structure would be easier to identify if 
you can trust your topology. In your case, initially using a topology 
with two copies of the same [molecule] will be a good point from which 
to start.

For example

[ moleculetype ]
Benzene 3

[ atoms ]

[ bonds ]


[ system ]
Two benzenes

[ molecules ]
Benzene 2


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