Md simulation analysis error

User discussions
1

GROMACS version: version 2018.1
GROMACS modification: Yes/No
Here post your question
ı want to simulated my structure 100 ns so I changed nsteps from 500000 to 50000000 in the mdp file .My simulation is over.but for analysis when I write these commands
gmx trjconv -s md.tpr -f md.xtc -o md_new.xtc -pbc mol -center
gmx rms -s md.tpr -f md_new.xtc -o rmsd-protein.xvg -tu ns
xmgrace rmsd.xvg

rmsd
rmsd792×612 3.21 KB

time is showing 1ns but ı run my simulation for 100 ns
my mdp file is
integrator = md
dt = 0.002
nsteps = 50000000
nstxtcout = 50000
nstvout = 50000
nstfout = 50000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 20
vdwtype = PME
rvdw = 1.2
rlist = 1.2
rcoulomb = 1.2
coulombtype = PME
;
tcoupl = Nose-Hoover
tc_grps = SOLU SOLV
tau_t = 1.0 1.0
ref_t = 303.15 303.15
;
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SOLU SOLV
;
so Could you help me that where I have made wrong please ?

2

WhatsApp Image 2022-01-30 at 19.00.15
WhatsApp Image 2022-01-30 at 19.00.152048×1151 298 KB

3

Did you recompile the .tpr file after changing nsteps? What does gmx check tell you about the contents of your .tpr and .xtc files?

4

gmx check -f step5.tpr it gives
Error in user input:
Invalid command-line options
In command-line option -f
File name ‘step5.tpr’ cannot be used for this option.
Only the following extensions are possible:
.xtc, .trr, .cpt, .gro, .g96, .pdb, .tng
so I check gmx check -f step5.xtc
Checking file step5.xtc
Reading frame 0 time 0.000

Atoms 146402

Precision 0.001 (nm)
Last frame 10 time 1000.000

Item #frames Timestep (ps)
Step 11 100
Time 11 100
Lambda 0
Coords 11 100
Velocities 0
Forces 0
Box 11 100
but md run I changed nsteps for 100 ns but after changed nsteps I couldnt recompile .tpr file also I dont know how to recompile .tpr file ?

5

After changing parameters in MDP file you need to use grompp to create the new tpr

6

I prepared my input file in charmm-gui.in step5_production.mdp file I changed num steps from 500000 to 50000000 for 100 ns and after that I used this command
gmx grompp -f step5_production.mdp -o step5.tpr -c step4.1_equilibration.gro -p topol.top -n index.ndx
before run md But result gives me just for 1 ns so Where is my fault ?

7

tpr
tpr1114×660 11.4 KB

After used command which mentioned above I checked step5.tpr file using this command gmx dump -s topol.tpr | more
I shared screen and in the tpr file nsteps is 50000000

8

What command did you to launch mdrun with?

If you check the log file, how many steps does it say it simulated?

9

After this command gmx grompp -f step5_production.mdp -o step5.tpr -c step4.1_equilibration.gro -p topol.top -n index.ndx,to run md simulation,I am using gromacs-slurm $GROMACS_DIR/bin/gmx_mpi mdrun -deffnm step5
and I checked log file which is step5.log ,it shows 500000 but why ? in my mdp file nteps=50000000,log file is 500000,but why ? where am I missing ?
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 500000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1270568627
emtol = 10
emstep = 0.01
niter = 20

10

This suggests to me that grompp does not produce the new .tpr. What is the output from that command? Any warnings or errors? Have you tried in a new directory without other files?