On 10/02/2011 10:54 AM, Rini Gupta wrote:
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?
Sure. See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
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
OK and what did you learn from the .log file about this? (Probably, it
restarted from the coordinates of the confout.gro, which loses precision
and some of the value of your initial equilibration)
and Pressure again increases up to 60 bar
No, it probably doesn't. See
http://www.gromacs.org/Documentation/Terminology/Pressure
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?
See
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4
I am using following topology file:
Can anyone please tell me if this topology is o.k to use
It's syntactically correct because grompp doesn't complain. Whether its
a sensible model physics can sometimes be rejected off-the-cuff, but
can't really be confirmed without actually testing against some other data.
Mark
; 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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