normal Position restraints doest not work!

  • James Starlight
  • James Starlight's Avatar Topic Author
  • Offline
  • Senior Boarder
More
11 months 2 weeks ago #7336 by James Starlight
James Starlight created the topic: Position restraints doest not work!
Dear Martini users!

I have faced with very strange issue. I am dealing with simulation of 20 GPCRs embedded within the big membrane.
During parametrization of the gpcr monomer I have defined posres on the backbone via -p backbone flag.

Now in my equilibration.mdp I have

define = -DPOSRES, -DRUBBER_BANDS

and in a itp of a protein

#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
3 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
7 1 POSRES_FC POSRES_FC POSRES_FC

Now I am runing a simulation and see in VMD that all GPCRs "dance" within the membrane even the posres flag is provided :-) Why the restraints does not work? How to prevent any movements of the proteins?

Thanks !

Gleb

Please Log in or Create an account to join the conversation.

  • peterkroon
  • peterkroon's Avatar
  • Away
  • Expert Boarder
More
11 months 2 weeks ago - 11 months 2 weeks ago #7339 by peterkroon
peterkroon replied the topic: Position restraints doest not work!
Hi,

you can still expect some movement, and IIRC only the backbone beads will be restrained. How much "dancing" do you see? Do they retain their relative positions?

Peter
Last Edit: 11 months 2 weeks ago by peterkroon.

Please Log in or Create an account to join the conversation.

  • James Starlight
  • James Starlight's Avatar Topic Author
  • Offline
  • Senior Boarder
More
11 months 2 weeks ago #7340 by James Starlight
James Starlight replied the topic: Position restraints doest not work!
Hi,


I fixed it via modification of the
define = -DPOSRES, -DRUBBER_BANDS # it was wrong!
to
define = -DPOSRES

:-)

James

Please Log in or Create an account to join the conversation.

  • peterkroon
  • peterkroon's Avatar
  • Away
  • Expert Boarder
More
11 months 2 weeks ago #7341 by peterkroon
peterkroon replied the topic: Position restraints doest not work!
Good catch! It might also work without the comma:
define = -DPOSRES -DRUBBER_BANDS

Please Log in or Create an account to join the conversation.

  • James Starlight
  • James Starlight's Avatar Topic Author
  • Offline
  • Senior Boarder
More
11 months 2 weeks ago #7342 by James Starlight
James Starlight replied the topic: Position restraints doest not work!
:-) could you also help me in the next topic regarding simulation of the flow along the CG membrane ??

James

Please Log in or Create an account to join the conversation.

More
3 months 1 week ago - 3 months 1 week ago #7617 by cm
cm replied the topic: Position restraints doest not work!
how i will fixed the position.
Last Edit: 3 months 1 week ago by cm.

Please Log in or Create an account to join the conversation.

Time to create page: 0.083 seconds