[gmx-users] Problems for Equilibration with 256 DPPC obtained from 64 DPPC

Yuhua Song yhsong at ccb.wustl.edu
Fri Nov 7 00:38:01 CET 2003

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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