[gmx-users] how to switch from NPT to NVT ensemble during equilibration
Rini Gupta
rinis.gupta at rediffmail.com
Thu Feb 10 00:54:10 CET 2011
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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