normal Lincs warning for protein-membrane system

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3 years 2 months ago #8893 by mpandey
Hi,

I was doing simulation of proteins (more than 1) on membrane, I minimized protein seperately and then used insane.py for making the system and also with cat command. But I was getting lot of Lincs warning (and inf Epot on some atoms). I also saw the nearest atoms and there was not water molecule or ions. I tried to build my initial system several times but it didn't work. Need some suggestions. I am attaching my mdp file for em.
thank you.

integrator = steep
dt = 0.03
nsteps = 10000
nstcomm = 1
nstxout = 0
nstvout = 0
nstlog = 100
nstxout-compressed = 1000
compressed-x-precision = 1000
nstcalcenergy = 1

em_tol = 10 (I changed this to 500 also but didn't work)
cutoff-scheme = Verlet
nstlist = 100
ns_type = grid
pbc = xyz

coulombtype = pme
rcoulomb = 1.2
epsilon_r = 15
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.2
constraints = none
constraint_algorithm = Lincs

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3 years 2 months ago #8894 by vainikka
Replied by vainikka on topic Lincs warning for protein-membrane system
Looks like there's some major issues with your starting configuration. Can you expand a bit on what you mean by the 'cat command' ?

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3 years 2 months ago #8895 by mpandey
Replied by mpandey on topic Lincs warning for protein-membrane system
Hi

I wanted to simulate a group of proteins on a membrane. For that, I used martinizer2 to convert the all-atom structure of the protein to CG. Then I used cat command to combine all the proteins and minimized this system in vacuum.
After that I used insane for building protein-membrane system using "python2 insane.py -u POPS:1 -u POPC:4 -l POPS:1 -l POPC:4 -pbc rectangular -x 40 -y 40 -z 20 -sol W -salt 0.15 -o test.gro -f All_protein.pdb -dm -13". But I was getting the Lincs error (inf Epot on some protein atoms) while doing EM.

I also used the "cat" command to combine minimized protein and membrane and then solvation ... but got the same error.

PS: I also tried to run a single protein with membrane and it worked but I am struggling while using a group of proteins.

Mayank

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