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Position restraints doest not work!
- James Starlight
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6 years 8 months ago #7336
by James Starlight
Position restraints doest not work! was created by James Starlight
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
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
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- peterkroon
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6 years 8 months ago - 6 years 8 months ago #7339
by peterkroon
Replied by peterkroon on 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
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: 6 years 8 months ago by peterkroon.
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- James Starlight
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6 years 8 months ago #7340
by James Starlight
Replied by James Starlight on 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
I fixed it via modification of the
define = -DPOSRES, -DRUBBER_BANDS # it was wrong!
to
define = -DPOSRES
:-)
James
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- peterkroon
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6 years 8 months ago #7341
by peterkroon
Replied by peterkroon on topic Position restraints doest not work!
Good catch! It might also work without the comma:
define = -DPOSRES -DRUBBER_BANDS
define = -DPOSRES -DRUBBER_BANDS
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- James Starlight
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6 years 8 months ago #7342
by James Starlight
Replied by James Starlight on 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
James
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- cm
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- Posts: 73
6 years 1 week ago - 6 years 1 week ago #7617
by cm
Replied by cm on topic Position restraints doest not work!
how i will fixed the position.
Last edit: 6 years 1 week ago by cm.
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