GROMACS version: 2018.1
GROMACS modification: No
I have a membrane in all atom scale and with two phospholipids that i produce using CHARMM-GUI, after i download the gromacs files i make the README with the minimization, equilibration and production steps an executable and i run it.
I noticed a lot of linc warnings since the beginning but no error occured in the sense that my simulation seems to continue running, but it is not, is stucked in the minimization step, when i see the final lines in the log file says: Initializing Parallel LINear Constraint Solver and some quotes but nothing is happening i try modifying some aspects of the mdp file but nothing seems to work.
I dont know what to do. I know that lincs warning are an early warning that the system is unstable but it doesnt seem that way. When i visualize the membrane seems normal and changing nstxout = 1 does nothing because the minimization step is not running.
I hope i can get help, i been with this trouble for weeks and i really dont understand what the problem is. Thank you in advanced
You will need to post what the actual messages are. Always provide more information than you think you need to. People you are asking to help can’t see what you see, don’t know what you know about what you are actually doing etc.
What is the command for the minimisation step? What is the output? Copy and paste the actual text.
For the minimization step i use:
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top
gmx_d mdrun -v -deffnm step6.0_minimization
The output until moment in the log file is:
Linking all bonded interactions to atoms
Initiating Steepest Descents
Atom distribution over 24 domains: av 12027 stddev 135 min 11856 max 12304
Started Steepest Descents on rank 0 Mon Oct 26 10:58:11 2020
Tolerance (Fmax) = 1.00000e+03
Number of steps = 5000
but it stop in that step and does not continue with the minimization.
my mdp file is:
define = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0
integrator = steep
emtol = 1000.0
nsteps = 5000
nstlist = 10
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = Cut-off
nstxout = 1
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = pme
rcoulomb = 1.2
lincs-order = 8
lincs-iter = 2
lincs_warnangle = 45
constraints = h-bonds
constraint_algorithm = LINCS