[gmx-users] box size changed

Nancy Deng jdeng at adrik.bchs.uh.edu
Thu Mar 1 01:13:17 CET 2007

Hi Mark,

Thanks for the quick response and the funny story :)

I indeed want to collect the possible comformation of a certain small 
molecule (a little car made of 35 atoms around 15 A in length) by MD. Since 
obvious to my understanding that in vacume or in water environment, the 
small molecule could behave quite different (i really want to see this 
happens :). So, my goal is to compare the difference of the two MD 
trajectories ( for example 5 ns or even longer) of the small molecule by 
Gromacs. But i am stuck even at the very beginning which i could never reach 
either New York or Detroit :(

In the case of no-water simulation, the box without water was generated by 
"editconf" but not followed by "genbox" to avoid water filling in.
The other box was consequently generated by "genbox" to contain 370 SPC 
water molecules. During the equilibration stage, the water particles seems 
prefer to roam away  from the originally centered small molecule, which i 
guess the reason to increase the overall size of the box...

Not sure whether this provides some useful input to help me out of the 
trouble :)



----- Original Message ----- 
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, February 28, 2007 3:42 PM
Subject: Re: [gmx-users] box size changed

> Nancy Deng wrote:
>> Dear All,
>> I am a very beginner of Gromacs and currently trying to run two small 
>> molecule (35 atoms) MD studies, one with water and the other without 
>> water (skip the "genbox" step).
>> Surprisingly, the box size of the system containing only small molecule 
>> (without water) kept shrink till the program crashed with the error of 
>> "one of the box vector has become shorter than twice the cut-off length".
>> However, the other system (water + small molecule) behave just opposite, 
>> i.e. the box size kept increased...
>> So, I am wondering whether you have any idear how to fix this??? Whether 
>> Gromacs is the right tool to sample small molecule conformational space.
> This is a bit like telling us you were going to drive somewhere in America 
> starting from Philadelphia. When you took the red car you ended up in New 
> York, and when you took the yellow car you found yourself in Detroit. 
> Apparently you didn't want to end up in either place, but you haven't told 
> us where you're trying to go or how you're trying to get there.
> Mark
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