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

[Matthew D Kim]

I adjusted it and it worked! Thank you so much.


On Mon, Jul 28, 2014 at 1:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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