[gmx-users] box size changed
tsjerkw at gmail.com
Thu Mar 1 22:33:33 CET 2007
After thinking (and reading) about pressure coupling, vacuum and pbc,
I would suggest to first set up these simulations with something well
defined, for instance a single amino acid (uncharged; you don't want
charges in vacuum). That will give you a feel for the way things
(should) work, by eliminating a possible source of error: your
If you have a working protocol, you can try to run it with your
molecule. Then you can assume that, if you encounter error, these are
due to your parameters, rather than to the protocol.
On 3/1/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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
> 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
> gmx-users mailing list gmx-users at gromacs.org
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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