[gmx-users] box size changed
erikm at xray.bmc.uu.se
Thu Mar 1 21:56:21 CET 2007
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.
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
> 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?
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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
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