[gmx-users] Re: EM-error

Anton Feenstra feenstra at few.vu.nl
Mon Sep 6 10:05:03 CEST 2004

Dinesh Pinisetty wrote:
> Respected Dr.Feestra,
>         I have taken the values from the literature.In Dr.Tielmanns website
> in the file we can see that 60 molecules were added for a single lipid.So
> in that way I should add 2880 molecules for 48 lipids.
>   I have a new question,When I try to shrink the box size using -box option
> in editconf will the co-ordinates also be automatically shrinked in that
> scale.I created a box with water of size 6.449 4.387,using editconf I
> reduced the box size of the bilayer as well to 6.449 4.387 it displays in
> the file the same box size.But when i visulaize it the water box and dppc
> box size are not the same.How can we get the co-ordinates of the bilayer as
> well according to box.I tried -scale option also as you told it did not
> work for me.I am sending you the files please check these once..........
> this file is only for bilayer.

editconf -box will only adjust the size of the periodic box, but does not change
the coordinates of the atoms at all (e.g., it is possible to make the box smaller
than the size of your bilayer or water slab).

You may have the number of water per lipid right, but the density of the bilayer
is still too low (large space between lipids), while the water is at the right
density. So, the bilayer will have to shrink, and a the same time the water has
to change its shape (contract in x-y and expand in z). This may cause difficulties
with, e.g., pressure coupling.	

For the rest, I am sorry to say I do not have the time to look again at your
coordinate files. Also, I have myself never simulated membranes. So, I am sorry
to have to refer you back to the gmx users list, and hope that someone else with
more experience in membrane simulations will find the time to help you further!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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 few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

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