[gmx-users] Re: doing simplest simulations

Nicolas Schmidt nicolas-schmidt at gmx.de
Sat Aug 11 14:12:21 CEST 2007

>> Second: Am I simulating fixed connections? 


I once wrote in a mail in may I think:

>> This may be a really simple question, I know, but still...
>> How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards):
>> WARNING 1 [file "ethane.itp", line 12]:
>>   No default Connect Bonds types, using zeros
>> Either way I'm not sure how the distance of these two atoms is processed, so there is NO parameter that is specifying this bond-type (and a constraint would be processed by gromacs, wouldn't it? And I don't want it to, cause I want the simulation to be as simple as possible)
>> By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this?
>> Thanks in advance to everyone who is replying, it's so hard when you're stuck. 
>[ constraint ]
>; i j type length
>1 2 1 0.15

So what's my mistake? I posted my .itp-file, do I have to do a change in the forcefield-files? When 'yes', what change? ;-)

>> Are my chosen options on the .mdp-file therefor correct? 
>By comparison with what?

To build up a fixed connection. What therefor to choose in the bonds section of the .mdp-file? constraints = none, all??? 

Is in the Electrostatics-section of the .mdp-file
>coulombtype = cut-off
>rcoulomb = 0
sufficient to not simulate any electrostatics?

If not, what else should I do? ;-)

to Mark:

thanks for your help, it's definitely not in the way that I'm refusing to take your advice 'bout the tutorials, but it's sometimes uneasy to find out some kind of an exception from the rule (fixed connections, no electrostatics, prefering speed to accuracy, and so on). Why doing an energy minimization when I equilibrate at an higher temperature and cool down afterwards? And of course I'm a newbie, otherwise I'd answer questions and not ask them. 

and most of all, I just have to do ONE set of simulations (with an various amount of molecules) to compare gromacs' speed in simulating large systems of simple gas molecules. I wanna do well, otherwise I'd just take what I got from the already finished simulations. But afterwards I'm done and won't bother you again. ;-) 

Thanks again.


posted the most recent .mdp-file and .itp-file as well.

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