[gmx-users] Problems for Equilibration with 256 DPPC obtained from 64 DPPC
jongejan at few.vu.nl
Fri Nov 7 08:19:01 CET 2003
Why don't you use the large system of DPPC bilayer provided
by Erik Lindahl in the GMX_Benchmark distribution?
This is already 'pre-equilibrated' and perhaps much easier
to start from. To get to a 256 DPPC system, you can cut away
Yuhua Song wrote:
> Hi, Anton:
> Thanks for your suggestion. After I first do the minimization of 64DPPC,
> then get the 256DPPC, the previous warning information disappear. That is
> great! But I met the new questions.
> 1) from the downloaded 64DPPC.pdb, the period box size is:47.245 42.319
> 99.505, but when I use "editconf" to center the structure, it shows that the
> system size is: 4.936 4.409 10.093. So, when I use genconf to generate
> 256DPPC, should I use the period box size from original file or the system
> size of DPPC64 to duplicate? When I use the system size to duplicate, seen
> from VMD that there are gap between the four pieces. When use the origial
> periodic box to duplicate, 256DPPC seems one intact piece, my concern is
> whether I use the period box of original 64DPPC period box to duplicate will
> cut some part of the molecule? If I use the system size to duplicate, the
> gap between 4 pieces will cause some problems? which way do you recommend me
> to do?
> 2)Also, after I minimize the dppc256, the sysmtem size became bigger, the
> period box size becames the two times of original 64DPPC periodic box size:
> 2*x, 2*y, Z. Now I am doing the equilibration, the period box size should be
> the system size or the the original 64DPPC size: 2*x, 2*y, Z?
> 3) After I do the minimization of 256 DPPC, does that mean the temperature
> is 0K, I have to warm the system up to 300K before the production run?
> 4) After I generate the 256DPPC file, I intend to put the 4 pieces of DPPC
> together, and 4 piece of water together in the *.gro file, in the format of
> DPPC SOL in gro. That is to say: in the *.top, it is: DPPC 64*4 SOL
> 1548*4. But when I use Grompp to generate the *.tpr file, it shows the
> warning information that the system has the non-zero total charge: 2.28e-05.
> After I change back to the orignial format: DPPC SOL DPPC SOL DPPC SOL DPPC
> SOL in the corresponding *.gro and *.top, this warning informaton disappear.
> I am wandering what is happen? If in the future, I want to make more large
> piece of DPPC such 256*4DPPC, if my current 256DPPC in the format of (DPPC
> SOL DPPC SOL DPPC SOL DPPC SOL ), could I still use "genconf" to duplicate?
> Thank you very much for your time and knowledge.
> ----- Original Message -----
> From: "Anton Feenstra" <feenstra at chem.vu.nl>
> To: <gmx-users at gromacs.org>
> Sent: Wednesday, November 05, 2003 10:43 AM
> Subject: Re: [gmx-users] Problems for Equilibration with 256 DPPC obtained
> from 64 DPPC
> > Yuhua Song wrote:
> > > Hi,
> > >
> > > With the 64DPPC.pdb bilayer download from Peter Tieleman's website,
> > > using command: genconf -nbox 2 2 1, I generate the 256 DPPC bilayer,
> > > Looking from the vmd, it seems that everything is fine. But when I use
> > > NPT way to do the equilibration,it crashed, the following info is show
> > > during the run:, I try to change: tau_p, rlist, rcoulomb, rvdw, but
> > > nothing can help. Could you please help me to take
> > > a look.
> > I would guess you have 'divided' some of your molecules across the
> > periodic boundaries, or rather, that is the way they already were in
> > the initial pdb file (from Peter's website). Then, when you 'multiply'
> > your systen using genconf, some lipids on the boundary will actually
> > be built from parts of different molecules (as defined in the topology),
> > and parts of one molecule will be in different locations in your box.
> > A solution could be to e.g. energy minimize Peter's pdb file first.
> > The minimization itself is not necessary, but as a side-effect, mdrun
> > will write the coordinates with all molecules 'whole'. That conformation
> > should be safe to multiply in genconf and used as starting point for
> > a simulation. (Perhaps there is a tool to do that, other than mdrun,
> > that may be easier, but none that I can think of now...)
> > --
> > Groetjes,
> > Anton
> > _____________ _______________________________________________________
> > | | |
> > | _ _ ___,| K. Anton Feenstra |
> > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> > | | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> > | | "If You See Me Getting High, Knock Me Down" |
> > | | (Red Hot Chili Peppers) |
> > |_____________|_______________________________________________________|
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NOTE: E-mail address has changed into
jongejan at few.vu.nl
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
e-mail: jongejan at few.vu.nl
tlf: +31 (0)20 4447612
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