[gmx-users] Positioning ions consistently

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 10 16:19:23 CEST 2002

On Wed, 10 Apr 2002, Anton Feenstra wrote:

>Lieven Buts wrote:
>>   I am trying to compare a number of small variations of
>> the same protein structure. The protein has a net charge of
>> -9 (well, -8.999999, anyway). When I add 9 Na ions to
>> the different variations, some of them are put in very
>> different positions. This might be an additional source
>> of variation between the starting structures.
>>   Would it be necessary/useful/pointless to try and
>> position the ions more consistently for the different
>> structures? Or maybe to leave the ions out altogether?
>My suggestion would be to leave them out. I think David also mentioned
>this a while ago on the list, the artefacts you can expect from adding 
>ions (e.g. insufficient sampling) and from other sources (forcefield, 
>limitations of Ewald LR forces) are bigger than from a net charge of 
>the system.
It was Erik who said that for small charge (1 or 2). However in this case 
I would definitely use ions, if only to please the future referees of your 
work, but also for Ewald summation etc. Check the concentration of ions in 
your box.

However I think the real question is why does genion give different 
results? Did you use the random option or not? If so the result is as 
expected, if not something is wrong.

In principle it is not very crucial, if these are supposed to be solvated 
ions. Then the -random option combined with a decent rmin (a bit larger 
than the default 0.6 nm) would give you the same results if you simulate 
long enough.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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