[gmx-users] rerun queries

[Dilraj Lama]

hello gmx-users,
                I have some queries regarding the usage and result of "rerun" option in mdrun
program of gromacs.

After simulation of my system (which comprised of a protein-peptide complex solvated in water),I
wanted to calculate the "nonbonded interaction" between the protein and the peptide.So i used the
rerun option of the "mdrun program" after making change in the energy group option of the ".mdp"
parameter file.

Initial ".mdp" file:
--------------------
energygrps = protein SOL

rerun ".mdp" file
---------------------
energygrps = protein peptide SOL

This was the only change I made.

I then preprocessed the input files using "grompp" program to generate ".tpr" file as:

grompp -f rerun.mdp -c .gro -n .ndx -p .top -o .tpr
-----------------------------------------------------
I used this ".tpr" file to run the "mdrun" program using rerun option as:

nohup mdrun -v -s .tpr -rerun .trr -o .trr -e .edr -g .log>& .job  &
------------------------------------------------------------------------

when i run this program i get the warning message as:

"Some frames do not contain velocities
Ekin Temperature and pressure are incorrect
The virial will be incorrect when constraint are present"

when i compare the ".log" file from the actual and rerun mdrun it looks like this:
                                        **********************
Actual run:
***********
 Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    1.66276e+02    7.68902e+02    1.56747e+03    3.56898e+02    9.03171e+02
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    2.06463e+04    1.73125e+05   -2.99305e+03   -1.04107e+06   -7.97644e+02
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    1.34345e-02   -8.47326e+05    1.30418e+05   -7.16908e+05    3.00277e+02
 Pressure (bar)
    8.54693e+02

Rerun run:
**********
 Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    1.66276e+02    7.68902e+02    1.56747e+03    3.56898e+02    9.03180e+02
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    2.06465e+04    1.73125e+05   -2.99305e+03   -1.04107e+06   -7.97597e+02
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    2.40138e-04   -8.47325e+05    1.30418e+05   -7.16908e+05    3.00277e+02
 Pressure (bar)
    8.55262e+02

The energy values for all terms are identical except for "Position Rest." , "Temperature" ,
*****************************************************************************************
"Pressure" and hence for "Potential" and "Total Energy".
********************************************************

Are Differences in "TEMPERATURE" and hence for "KINETIC ENERGY" and also for "PRESSURE" arising
because i am not saving the velocities in the actual ".trr" at every step at which i am saving the
coordinates as mentioned in the WARNING message ????????

Steps for saving coordinates and velocities in the actual ".mdp" file
-----------------------------------------------------------------------
nstxout             =  500
nstvout             =  50000

Also why there is differences in the "POSITION RESTRAINT" term???????

Regarding Position restraint, i have the following query also.
*************************************************************

In my simulation i have run the dynamics where i have restraint the whole protein-peptide complex
(the log file of which i have shown above) and another where i have restraint only some set of
atoms (About 25).

The log files of which are as follows:
***************************************
Actual run:
**********
Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    2.11614e+03    2.90662e+03    1.62946e+03    1.09761e+03    8.35370e+02
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    2.04806e+04    1.10491e+05   -3.01009e+03   -8.17252e+05   -3.33932e+04
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    1.11632e-04   -7.14099e+05    1.30546e+05   -5.83553e+05    3.00572e+02
 Pressure (bar)
    1.19195e+02

Rerun run:
**********
Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    2.11614e+03    2.90662e+03    1.62946e+03    1.09761e+03    8.35378e+02
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    2.04808e+04    1.10491e+05   -3.01009e+03   -8.17252e+05   -3.33933e+04
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    1.11632e-04   -7.14099e+05    1.30546e+05   -5.83553e+05    3.00572e+02
 Pressure (bar)
    1.19225e+02

In this run the difference i find is that the "POSITION RESTRAINT" term and hence the "POTENTIAL"
*************************************************************************************************
term are identical in botht the runs.
************************************

So why is it that the "Position restraint" term differs in both the runs when i restraint the
entire protein-peptide system whereas the "Position restraint" term in identical in both the runs
when i restrain only a set of atoms from the protein-peptide complex????????

Sorry if i query has gone too long.

Thank you.
-- 
Dilraj Lama,
PhD Student,
c/o Dr. R. Sankararamakrishnan,
Bioinformatics and Biomolecular Simulation Lab,
Dept. of BSBE,IIT-Kanpur,
UP-208016:India