[gmx-users] PRODRG -cgnr

[Matthew D Kim]

Oh gosh sorry, I accidentally replied to someone's post rather than
starting a new thread.


On Mon, Jul 28, 2014 at 12:16 PM, Matthew D Kim <mdkim at wesleyan.edu> 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!)
>
> -Matthew
>
>
>
> On Mon, Jul 28, 2014 at 11:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/28/14, 10:06 AM, Atila Petrosian wrote:
>>
>>> Dear Justin
>>>
>>> Thanks for your quick answers.
>>>
>>> Based on your answers, what should Ido?
>>>
>>> You have more experience than me in these regards. What is your
>>> suggestion
>>> about my ligand molecule?
>>>
>>>
>> Gromos96 parametrization is predicated upon transferring pieces of
>> molecules into larger pieces.  So you need to find a suitable model
>> compound that has known experimental target data; ideally heat of
>> vaporization and free energy of solvation.  Such information is available
>> for a compound like acethydrazide, which takes care of the most complex
>> part of your molecule.  Tune the nonbonded parameters to reproduce the
>> experimental data, then refine the bonded parameters as needed to
>> reproduce, e.g. crystal data and torsional energy profiles.  Then you can
>> import the new parameters into the whole molecule.
>>
>> -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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>