[gmx-users] Changing .mdp options in continuation run problems

[Matthew D Kim]

Hi there,

I am having problems with extending my simulation after changing the .mdp
file options in GROMACS 4.6.
As per the instructions in the online Manual, I did

*grompp -p system.top -f md.npt-gpu-mod.mdp -c 300monolayer.tpr -o
x340monolayer.tpr -t 300monolayer.cpt*

[*note: I had to specify the topology file for grompp, as it kept trying to
use a topology file that does not exist. but this question isn't about
that!*]

When I grompp, GROMACS returns this:

"
Generated 0 of the 406 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'DPPC'
Excluding 1 bonded neighbours molecule type 'W'
Reading file 300monolayer.tpr, VERSION 4.6 (single precision)
Reading file 300monolayer.tpr, VERSION 4.6 (single precision)
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 101314      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Simulated annealing for group DPPC: Single, 6 timepoints
Time (ps)   Temperature (K)
      0.0      300.0
 100000.0      310.0
 200000.0      320.0
 300000.0      330.0
 400000.0      335.0
 500000.0-     340.0
Simulated annealing for group W: Single, 6 timepoints
Time (ps)   Temperature (K)
      0.0      300.0
 100000.0      310.0
 200000.0      320.0
 300000.0      330.0
 400000.0      335.0
 500000.0-     340.0
Number of degrees of freedom in T-Coupling group DPPC is 95759.27
Number of degrees of freedom in T-Coupling group W is 295959.72
Determining Verlet buffer for an energy drift of 0.005 kJ/mol/ps at 340 K
Calculated rlist for 1x1 atom pair-list as 1.779 nm, buffer size 0.579 nm
Set rlist, assuming 4x4 atom pair-list, to 1.549 nm, buffer size 0.349 nm
Reading Coordinates and Box size from old trajectory
Will read whole trajectory
Velocities generated: ignoring velocities in input trajectory
Last frame         -1 time 1000000.000
Using frame at t = 1e+06 ps
Starting time for run is 0 ps
This run will generate roughly 139 Mb of data
"
after I do this, I submit it to my university's cluster using

*mdrun -deffnm x340monolayer -s x340monolayer.tpr *

I checked the simulation after it started running using g_energy -f
x340monolayer.edr and looked at the time of the simulation, and indeed it
DID start at 0ps instead of 1e+06ps.

*My question is: *Why is the starting time for the run* 0 ps? *

(I am sorry if this has been asked/answered before, I sifted through the
forums but could not find anything!)

--Matthew