- Posts: 98
Martini system blowing up (lincs warnings)
- vikasdubey1008
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7 years 6 months ago #5933
by vikasdubey1008
Martini system blowing up (lincs warnings) was created by vikasdubey1008
Hi everyone,
I am using MARTINI polarisable water model. I have created at very large lipid patch of mixed bilayer (8190 lipids) using insane.py containing ( 80% DOPC and 20 % DOPS) then I tried to add ions to neutralise my system. In the process of generating *.tpr, I got a mismatch warning :
Warning: atom name 39313 in topol.top and DOPC-DOPS.gro does not match (CNO - CN0)
Warning: atom name 39325 in topol.top and DOPC-DOPS.gro does not match (CNO - CN0)
Warning: atom name 39337 in topol.top and DOPC-DOPS.gro does not match (CNO - CN0)
Which I ignored using maxwarn.
Then I tried doing energy minimization.
integrator = steep
dt = 0.02
nsteps = 5000
nstxout = 1000
nstvout = 1000
nstlog = 1000
nstxtcout = 1000
xtc-precision = 100
energygrps = membrane solute
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = membrane solute
tau-t = 1.0 1.0
ref-t = 310 310
I have tried lot of lots of tweaks e.g. step size but dint work. I always ended with up lincs warnings.
Another thing that I tried that I created a small patch 512 lipids and replicated it using genconf. Again, I got lincs warnings and simulation crashed. What could I do be the possible reasons ? How can I resolve this issue ?
Thanks,
I am using MARTINI polarisable water model. I have created at very large lipid patch of mixed bilayer (8190 lipids) using insane.py containing ( 80% DOPC and 20 % DOPS) then I tried to add ions to neutralise my system. In the process of generating *.tpr, I got a mismatch warning :
Warning: atom name 39313 in topol.top and DOPC-DOPS.gro does not match (CNO - CN0)
Warning: atom name 39325 in topol.top and DOPC-DOPS.gro does not match (CNO - CN0)
Warning: atom name 39337 in topol.top and DOPC-DOPS.gro does not match (CNO - CN0)
Which I ignored using maxwarn.
Then I tried doing energy minimization.
integrator = steep
dt = 0.02
nsteps = 5000
nstxout = 1000
nstvout = 1000
nstlog = 1000
nstxtcout = 1000
xtc-precision = 100
energygrps = membrane solute
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = membrane solute
tau-t = 1.0 1.0
ref-t = 310 310
I have tried lot of lots of tweaks e.g. step size but dint work. I always ended with up lincs warnings.
Another thing that I tried that I created a small patch 512 lipids and replicated it using genconf. Again, I got lincs warnings and simulation crashed. What could I do be the possible reasons ? How can I resolve this issue ?
Thanks,
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- bart
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7 years 6 months ago #5965
by bart
Replied by bart on topic Martini system blowing up (lincs warnings)
Hi vikasdubey1008,
I think the epsilon you use e=15 is for the standard MARTINI and not the polarisable system. U should use the value behind the semicolon e=2.5. This could solve your problem. I also see you use the coulomb type=reaction-field which is fine, but if proper electric interactions are important you could consider using PME, though this will be considerably slower (which might be a problem considering your system size).
Second I think it would be wise to start with a considerable smaller patch and work out what you want to do. Then if that works, make the larger system and run all the things you have tested before on the smaller one.
Cheers,
Bart
PhD student at the MARTINI lab
I think the epsilon you use e=15 is for the standard MARTINI and not the polarisable system. U should use the value behind the semicolon e=2.5. This could solve your problem. I also see you use the coulomb type=reaction-field which is fine, but if proper electric interactions are important you could consider using PME, though this will be considerably slower (which might be a problem considering your system size).
Second I think it would be wise to start with a considerable smaller patch and work out what you want to do. Then if that works, make the larger system and run all the things you have tested before on the smaller one.
Cheers,
Bart
PhD student at the MARTINI lab
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- peterkroon
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7 years 6 months ago #5968
by peterkroon
Replied by peterkroon on topic Martini system blowing up (lincs warnings)
In addition, if the minimization still won't work, replace the constraints in the PW molecule for stiff bonds and try running the minimization again. Afterwards, change them back to constraints for your equilibration/production.
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- yogi@martini
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- Posts: 31
7 years 1 month ago #7194
by yogi@martini
Replied by yogi@martini on topic Martini system blowing up (lincs warnings)
Sometimes LINCS warning comes because of the beads overlap. Try reducing the time step during minimization, once system relaxes a little bit you can increase time step.
Hope this helps.
Hope this helps.
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