[gmx-users] guanidinium in water

[Justin Lemkul]

Please don't hijack an unrelated thread with a new question.  I am re-titling 
this message; in the future, just send a new email when you have a new question.

On 4/27/14, 11:11 AM, Swetha Srinivasan wrote:
> Hi Lemkul,
>
> I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ?
>

FudgeQQ is explained in the manual.  Beyond that, you need to provide more 
details.  What is in your topology?  Did you create it yourself, or did you get 
it from some other source?  What is the *exact* error message from grompp 
(copied and pasted from the terminal)?

As for solvent removal, you'll have to tell us how you added solvent in the 
first place.  Presumably this was done with genbox, in which case you can use 
-maxsol, but that's often not a good idea because it will leave voids in the 
simulation box.  If the box is too large, you'll have to set up an appropriate 
one with editconf (or possibly genbox, but I'm still guessing here because you 
haven't provided any of your commands).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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