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

[Justin Lemkul]

On 7/28/14, 1:21 PM, Matthew D Kim wrote:
> 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!)
>

The default value of tinit in the .mdp file is zero.  If you didn't specify 
another value, then that's what you'll get.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================