[gmx-users] Re: EM-error

Anton Feenstra feenstra at chem.vu.nl
Fri Sep 3 09:46:01 CEST 2004

Dinesh Pinisetty wrote:
> Respected Dr.Anton Feestra,
>            I am very sorry for disturbing you.I just want to send my files
> to you,could you please check them out and tell me the mistake I have
> made.My system consists of DPPC membrane and water created in a box is
> added on either side of the membrane.
> You just check them out and tell where exactly I am making
> mistake.It won't take time for people like you to get the mistake.

I've had a short glance at your files.

This is what I noticed:
- your .top file sais 'DPPC in water', but there are no 'SOL' molecules added.
- your .gro file probably contains much too much water for the lipids.

The lipids are still spaced far apart (due to your genconf procedure), and will
need to equilibrate to the proper areal density (nm^2/headgroup or whatever).
Probably you'd need to do that before you add water. Be aware that this may take
very long (maybe 10-100 ns!). You could speed it up a bit by 'compressing' the
lipids first, e.g. using editconf -scale, but if you compress to much in this way,
you may not be able get the md started. ON the other hand, the very low density
you have now may cause pressure coupling to rapidly compress the system for you,
giving possibly the same problems.

So, I'm sorry I do not have a clear-cut solution for you, and it seems to me I
have not offered anything that wasn't already discussed on the list. Still, I
hope you can get things running - I've heard from other people that they sometimes
needed up to half a year to get their membrane running, but I have not actually
heard from someone who didn't get it running in the end (so there is hope!).

[PS, I've cc-ed this back onto the list as well.]


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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)                               |

More information about the gromacs.org_gmx-users mailing list