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Unable to form a bilayer
- Rajat Desikan
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12 years 8 months ago #775
by Rajat Desikan
Unable to form a bilayer was created by Rajat Desikan
I am a new gromacs user. I want to use Martini for my future work. I followed the instructions in the bilayer self assembly tutorial. There were no problems during simulation. But after 27 ns simulation, the final minimized.gro did not resemble a bilayer. So I ran a simulation for 200 ns. Even now, as viewed in ngmx, a bilayer has not formed. How do I go about this? Thanks
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12 years 8 months ago #777
by djurre
Replied by djurre on topic Unable to form a bilayer
Dear Rajat,
Several things might have happened. I need a bit more information to know what is going on.
-Minimzed.gro is a strange name for a simulation output. Are you sure you're not looking at the output file of the minimization run?
-If the structure is not a bilayer, what does it look like?
-Is the 200ns simulation an continuation of the first run? Did you try to start a new simulation with different seed? (eg in you mdp file, try: gen_vel = yes, gen_seed = -1).
Groetnis,
Djurre
Several things might have happened. I need a bit more information to know what is going on.
-Minimzed.gro is a strange name for a simulation output. Are you sure you're not looking at the output file of the minimization run?
-If the structure is not a bilayer, what does it look like?
-Is the 200ns simulation an continuation of the first run? Did you try to start a new simulation with different seed? (eg in you mdp file, try: gen_vel = yes, gen_seed = -1).
Groetnis,
Djurre
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12 years 8 months ago #778
by Rajat Desikan
Replied by Rajat Desikan on topic Unable to form a bilayer
Dear Djurre
Thanks for the quick reply. In the self assembly tutorial, the following is given
"Now, you are ready to run the self-assembly MD simulation. About 25 ns should suffice.
grompp -f md.mdp -c minimised.gro -p dspc.top -maxwarn 10
mdrun -v"
The output will be stored in minimised.gro itself since we have not specified any other output name in mdrun. Is that right?
The structure just looks random with the water molecules more or less concentrated at the lower left corner of the box. I can send you the .gro file if that is possible. No, I did not try a different seed. Should I do it? As I said, I only learnt Gromacs a month ago, so I am a bit raw. Thanks again for your help :)
Thanks for the quick reply. In the self assembly tutorial, the following is given
"Now, you are ready to run the self-assembly MD simulation. About 25 ns should suffice.
grompp -f md.mdp -c minimised.gro -p dspc.top -maxwarn 10
mdrun -v"
The output will be stored in minimised.gro itself since we have not specified any other output name in mdrun. Is that right?
The structure just looks random with the water molecules more or less concentrated at the lower left corner of the box. I can send you the .gro file if that is possible. No, I did not try a different seed. Should I do it? As I said, I only learnt Gromacs a month ago, so I am a bit raw. Thanks again for your help :)
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12 years 8 months ago #779
by djurre
Replied by djurre on topic Unable to form a bilayer
Dear Rajat,
The option '-c' of grompp (minimized.gro in your case) is the input structure. I no options are given to mdrun it will save the final frame of the simulation as 'confout.gro' and the trajectory as 'traj.xtc' and/or 'traj.trr'. Have a look at those files.
I hope it looks better now! (else, let me know).
Groetnis,
Djurre
The option '-c' of grompp (minimized.gro in your case) is the input structure. I no options are given to mdrun it will save the final frame of the simulation as 'confout.gro' and the trajectory as 'traj.xtc' and/or 'traj.trr'. Have a look at those files.
I hope it looks better now! (else, let me know).
Groetnis,
Djurre
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12 years 8 months ago #780
by Rajat Desikan
Replied by Rajat Desikan on topic Unable to form a bilayer
Oh yes it does.:) Thank you so much.:)...only one DSPC molecule is out of the bilayer...
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12 years 8 months ago #781
by Rajat Desikan
Replied by Rajat Desikan on topic Unable to form a bilayer
I have another doubt. In the bilayer system setup, we have
genbox -ci dspc_single.gro -nmol 128 -box 7.7 7.7 7.7 -try 100 -o 128_noW.gro
But in gromacs manual, it says that nmol is the number of 'extra' molecules to be added. So shouldn't nmol be 127 since we already have one molecule?
And why is the box of size 7.7 7.7 7.7? If I wanted to form a DPPC bilayer, how would it change?
Thanks again.
genbox -ci dspc_single.gro -nmol 128 -box 7.7 7.7 7.7 -try 100 -o 128_noW.gro
But in gromacs manual, it says that nmol is the number of 'extra' molecules to be added. So shouldn't nmol be 127 since we already have one molecule?
And why is the box of size 7.7 7.7 7.7? If I wanted to form a DPPC bilayer, how would it change?
Thanks again.
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12 years 8 months ago #783
by djurre
Replied by djurre on topic Unable to form a bilayer
-You don't already have one molecule, since there is no -cp/-cs option given (that would be the 'first' molecule).
-The box size is like that because we found it to be right by trial and error. Since the system will relax (and the volume change) it will not really change if you go to DPPC.
-The box size is like that because we found it to be right by trial and error. Since the system will relax (and the volume change) it will not really change if you go to DPPC.
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12 years 8 months ago #784
by Rajat Desikan
Replied by Rajat Desikan on topic Unable to form a bilayer
Thanks for the reply :) That totally cleared it up.
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