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

Anton Feenstra feenstra at chem.vu.nl
Tue Nov 11 09:54:01 CET 2003

Yuhua Song wrote:
> 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?

The short answer is: just use genconf.

The long answer is:
System size that editconf reports is the size that the atoms occupy together,
measured along the three axes (x, y, z). This is normally bigger than actual
box dimensions (as found in the .pdb or .gro files), because due to the
periodicity atoms will stick out on all sides of the box. When 'multiplying'
your system you want to preserve periodicity, so you need to use the box
dimensions from the files (note, that numbers in .pdb files are Angstrom, and
in .gro are in nm!). The gaps you see are a real problem that you don't want!
genconf will not cut away any of your molecules.

> 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?

If you do not change anything about the box sizes in the files, all should
work as it is. In any case, 'system size' is not the parameter to use.
So, the periodic box of dppc256 should be 2*x, 2*y, z compared to dppc64.

> 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?

No, during minimization there is no velocity on the atoms, hence no kinetic
energy, hence no temperature. There are two ways to get the right system
temperature: generate velocities from a maxwell distribution at the
temperature you want (there is an option in the .mdp for that, and this
is the way most people do it), or heat your system from 0K to the temperature
using simulated annealing (tricky, I don't normally do that).

> 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?

2.28e-5 reads as 0.0000228 which would be near enough to zero for me (but
grompp doesn't know that)! This is a round-off error due to adding a large
number of charges (for each atom), and will depend on the order in which
they are added. That would explain what you describe.
And, yes, you can multiply your 256dppc again using genconf, independent
on the order of the molecules. You can always sort them again if you want.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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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