[gmx-users] box size changed

Nancy Deng jdeng at adrik.bchs.uh.edu
Thu Mar 1 19:12:30 CET 2007

Thanks Mark!!

... Yes, I did play with the demo and run some tutorial. In my small 
molecule study, I got the .gro (with polar H only) and .itp file from the 
PRODRG sever. Then I used Gamess to calculate the partial charges to the 
polar-H containing molecule, and the new charges were updated in the .itp 

In the case of vacumm MD:
A: the box  size at the beginning of equilibration is 2.58 x2.50 x 2.55, and 
reached 1.93x 1.87x 1.91A^3 at 1ps and the calculation stopped soon after.
B: I used NPT ensemble as described in the below mdp file: ( I am wondering 
whether NVT will fix the size... But how, please????)
            title               = noWater
            cpp                 =  /lib/cpp
            constraints         =  hbonds
            constraint-algorithm = shake
            integrator          =  md
            dt                  =  0.002    ; ps !
            nsteps              =  25000    ; total 50ps for equilibration
            nstcomm             =  1
            comm_grps           =  MON ; name of the small molecule
            nstxout             =  1000    ; output coordinates every 2 ps
            nstvout             =  1000    ; output velocity every 2ps
            nstfout             =  0
            nstxtcout           =  1000
            nstlog              =  1000
            nstenergy           =  1000
            nstlist             =  10
            ns_type             =  grid
            coulombtype         =  PME
            rlist               =  0.5
            rcoulomb            =  0.5
            rvdw                =  0.5
            fourierspacing      =  0.12
            pme_order           =  4
            optimize_fft        =  yes
            ; Berendsen temperature coupling is on in two groups
            Tcoupl              =  berendsen
            tc-grps             =  MON
            tau_t               =  0.1
            ref_t               =  300
            ; Energy monitoring
            energygrps          =  MON
            ; Pressure coupling is on
            Pcoupl              =  berendsen
            pcoupltype          =  isotropic
            tau_p               =  1
            compressibility     =  4.5e-5
            ref_p               =  1.0
            ; Generate velocites is on at 300 K.
            gen_vel             =  yes
            gen_temp            =  300.0
            gen_seed            =  173529

While in my othe system with water involved, I use NPT ensemble as well. The 
orginal soaked box size is 2.29 x 2.71 x 2.44, but reached to 3.36 x 3.98x 
2.44 after equilibration. Now it was crashed with 'segmentation fault" and a 
warning in the log file as " the box size exploding".

Very grateful for your advice and help!!!


----- 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 5:15 PM
Subject: Re: [gmx-users] box size changed

> Nancy Deng wrote:
>> 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 :)
> We need to know the kind of simulation you're attempting (ensemble, etc.), 
> the size box you're using and its density, your equilibration regime, 
> whether you got any warnings from grompp, and probably other stuff I can't 
> think of now, in order to tell where you're breaking things.
> Have you tried the tutorial material?
> Mark
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