[gmx-users] pressure and potential energy

[abhishek khetan]

No I was never warned about anything like that.
The output I get after grompp for the NVT continuation run is:
-------------------------------------------------------------------------------------------------
Command line:
  gmx_mpi grompp -f nvt.mdp -c dme_nvt.gro -t dme_nvt.cpt -o nvt.tpr

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Setting the LD random seed to 451659651
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DME'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:    64      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 3069.00
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.100 nm, buffer size 0.000 nm
Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame         -1 time 1000.000
Using frame at t = 1000 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 20x20x20, spacing 0.111 0.111 0.111
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 6 Mb of data
-------------------------------------------------------------------------------------------------

And the output when using the NVT data in the NPT grompp is:

-------------------------------------------------------------------------------------------------
Command line:
  gmx_mpi grompp -f npt.mdp -c dme_nvt.gro -t dme_nvt.cpt -o npt.tpr

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Setting the LD random seed to 846700063
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DME'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:    64      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 3069.00
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.100 nm, buffer size 0.000 nm
Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame         -1 time 1000.000
Using frame at t = 1000 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 20x20x20, spacing 0.111 0.111 0.111
Estimate for the relative computational load of the PME mesh part: 0.22
This run will generate roughly 6 Mb of data
-------------------------------------------------------------------------------------------------

Both times when I use mdrun, there are no special lines saying that the
time step is large or whatever. yeah, you're spot on, I'm not using any
constraints and/or restraints, nor any refcoord_scaling. Do you think that
is where the problem originates? I discussed this at length on the forum (
http://permalink.gmane.org/gmane.science.biology.gromacs.user/83291) and
from what i learned, i really had no reason to use constraints/restraints
for my nonaqueous solvent system.

Im trying to increase the fourier grid density and then rerun the
simulations. It would be very kind if you can educate me a bit here on
getting to procedure to equilibration and production MD runs. Thanks very
much in advance.

Hi,
>
> Did grompp warn you that your time step was too large for a system without
> constraints? What did you do about that?
>
> Mark
>
> On Thu, 24 Mar 2016 00:28 abhishek khetan <askhetan at gmail.com> wrote:
>



-- 
MfG,
abhishek