[gmx-users] box size changed

[Erik Marklund]

Just as Tsjerk suggested; take the time to think about what pressure  
coupling of a vacuum system would do. The online manual shows how to  
easily turn P-coupling off and keep the box size fixed. Another thing  
to think about is whether you really want pbc for a vacuum simulation.

Good luck

/Erik

1 mar 2007 kl. 19.12 skrev Nancy Deng:

> 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 file.
>
> 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!!!
>
> Nancy
>
>
>
>
> ----- 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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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys