[gmx-users] PRODRG -cgnr

[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



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.
>