[gmx-users] how to switch from NPT to NVT ensemble during equilibration

[Rini Gupta]

Dear gmx users,

 I am using gromacs (version 4.0.7) first time
 to setup a 2-butoxyethanol-water simulation.
 I created topology and coordinate file for BE using AUTOMATED TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield.
 Then a generated a box containing 20 BE and 480 water molecules using
 genbox.

 When I performed energy minimization followed by mdrun using NPT ensemble.
I get

Potential Energy  = -1.56616474544600e+04 
Maximum force     =  9.72854664927673e+02 on atom 910


Then, I run for 200ps equlibration using NPT ensemble with Berendsen 
thermostat and P coupling
I want to use NVT ensemble for my calculations, so it is ok to switch from NPT to NVT ensemble during equilibration?
First, I did equilibation for 200ps using NPT ensemble
I get 
 Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
   -1.81617e+04    3.00167e+02   -4.32808e+00    0.00000e+00
and,
My box length changes from 2.7 nm to 2.6503 nm

Then using state.cpt with mdrun I run for another 200ps using NVT settings in .mpd file ( I turn off the P-coupling).

I use the following commands:
I regenerated new .tpr file 
grompp_d_mpi -f grompp.mdp -c confout.gro -p topol.top -o topol.tpr

mdrun_d_mpi -s topol.tpr -cpi state.cpt

 Simulation is completed with warning

WARNING: The checkpoint state entries do not match the simulation,
         see the log file for details

and Pressure again increases up to 60 bar

 Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
   -1.82304e+04    2.99992e+02    6.20706e+01    0.00000e+00


I want to know if this is a right procedure for switching ensemble.
do i need to generate new velocities during second run using NVT ensemble?
If this is correct, how can i reach the target of Pressure 1 bar using this approach?

I am using following topology file:
Can anyone please tell me if this topology is o.k to use


; Include forcefield parameters
#include "ffG53a6.itp"

[ moleculetype ]
; Name   nrexcl
G269     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OE    1    G269      O    1   -0.345  15.9994
    2   CH2    1    G269      C    1    0.151  14.0270
    3   CH2    1    G269      C    1    0.194  14.0270      ;  0.000
    4   CH2    1    G269      C    2    0.231  14.0270
    5    OA    1    G269      O    2   -0.617  15.9994
    6     H    1    G269      H    2    0.386   1.0080      ;  0.000
    7   CH2    1    G269      C    3   -0.035  14.0270
    8   CH2    1    G269      C    3    0.143  14.0270
    9   CH3    1    G269      C    3   -0.108  15.0350      ; -0.000
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1430   8.1800e+06
    1    3    2   0.1430   8.1800e+06
    2    4    2   0.1520   5.4300e+06
    3    7    2   0.1520   5.4300e+06
    4    5    2   0.1430   8.1800e+06
    5    6    2   0.1000   2.3200e+07
    7    8    2   0.1530   7.1500e+06
    8    9    2   0.1530   7.1500e+06
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
    1    5    1
    1    8    1
    2    6    1
    2    7    1
    3    4    1
    3    9    1
[ angles ]
;  ai   aj   ak  funct   angle     fc
    2    1    3    2    109.50   380.00
    1    2    4    2    109.50   320.00
    1    3    7    2    109.50   320.00
    2    4    5    2    111.00   530.00
    4    5    6    2    108.53   443.00
    3    7    8    2    111.00   530.00
    7    8    9    2    111.00   530.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle     fc
[ dihedrals ]
;  ai   aj   ak   al  funct    ph0      cp     mult
    3    1    2    4    1      0.00     1.26    3
    2    1    3    7    1      0.00     1.26    3
    1    2    4    5    1      0.00     2.53    3
    1    3    7    8    1      0.00     3.77    3
    2    4    5    6    1      0.00     1.26    3
    3    7    8    9    1      0.00     3.77    3
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions




; Include water topology
#include "spce.itp"
[ system ]
; Name
BE in Water

[ molecules ]
; Compound      #mols
G269              20
SOL               480

Please help me in this regard.

Thanks and Regards,
Rini

----------------
Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver


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