normal minimization

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4 years 8 months ago #3927 by Pazmino
minimization was created by Pazmino
I am new to GROMAS, I will really appreciate your help.

I'm trying to minimize the vesicle generated in the tutorial with no luck.
This is my minimization script


; Define can be used to control processes
define = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 10.0 ; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps = 1000 ; Maximum number of (minimization) steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstcomm = 1

rlist = 1.4

coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15

vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2

tc-grps = system
tau-t = 4.0
ref-t = 310

pcoupl = berendsen ; no
pcoupltype = isotropic ; semiisotropic
tau-p = 4.0 ; 4.0 4.0
compressibility = 3e-4 ; 3e-4 0.0
ref-p = 0.0 ; 0.0 0.0

Thanks for your help,

B

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4 years 8 months ago #3934 by Clement
Replied by Clement on topic minimization

Pazmino wrote: I'm trying to minimize the vesicle generated in the tutorial with no luck.

What does that mean? How do you run this "minimization script"? What error do you get? At what point does it stop/crash/fail?

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4 years 8 months ago #3944 by Pazmino
Replied by Pazmino on topic minimization
Thanks for your reply, I really appreciated :)

I am following the tutorial in lipids:
and I generated .gro and .top file with the python martini_vesicle_builder.py

martini_vesicle_builder.py 12.5 DPPC:DUPC,60:40 43 1> system.gro 2> system.top
Then I just minimize with

grompp -v -f mini.mdp -c system.gro -p system.top -o system-min.tpr
mdrun -v -deffnm system-min -c system-min.gro

The script runs…
The potential energy doesn't decrease, I guess is because

Step= 56, Dmax= 2.1e-01 nm, Epot= 3.96021e+08 Fmax= 2.47724e+09, atom= 7248
Step 57, time 2.28 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003337, max 0.128852 (between atoms 127289 and 127287)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
127287 127285 31.9 0.4930 0.5304 0.4930
127288 127287 60.8 0.2720 0.2911 0.2720
127289 127287 46.3 0.3460 0.3906 0.3460
Step= 57, Dmax= 2.5e-01 nm, Epot= 3.68623e+08 Fmax= 1.18876e+08, atom= 7248

At this step this warnings start and then they are more often.

It does not crash but pot energy never goes down and if I let it run more the round structure of the vesicle is completely lost…

I'm pretty sure that once the vesicle is "melted", it is very difficult to go back to be a vesicle…

So, there is something that I am missing in interactions in the equilibration script that I do not know… Help!

Thanks for your help,

B

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