Dear gmx users,<br />
<br />
I am using gromacs (version 4.0.7) first time<br />
to setup a 2-butoxyethanol-water simulation.<br />
I created topology and coordinate file for BE using AUTOMATED TOPOLOGY BUILDER server.<br />
It created a topology file (for united atom) compatible with GROMOS ffG53a6 forcefield.<br />
Then a generated a box containing 20 BE and 480 water molecules using<br />
genbox.<br />
<br />
When I performed energy minimization followed by mdrun using NPT ensemble.<br />
I get<br />
<br />
Potential Energy = -1.56616474544600e+04 <br />
Maximum force = 9.72854664927673e+02 on atom 910<br />
<br />
<br />
Then, I run for 200ps equlibration using NPT ensemble with Berendsen <br />
thermostat and P coupling<br />
I want to use NVT ensemble for my calculations, so it is ok to switch from NPT to NVT ensemble during equilibration?<br />
First, I did equilibation for 200ps using NPT ensemble<br />
I get <br />
Total Energy Temperature Pressure (bar) Cons. rmsd ()<br />
-1.81617e+04 3.00167e+02 -4.32808e+00 0.00000e+00<br />
and,<br />
My box length changes from 2.7 nm to 2.6503 nm<br />
<br />
Then using state.cpt with mdrun I run for another 200ps using NVT settings in .mpd file ( I turn off the P-coupling).<br />
<br />
I use the following commands:<br />
I regenerated new .tpr file <br />
grompp_d_mpi -f grompp.mdp -c confout.gro -p topol.top -o topol.tpr<br />
<br />
mdrun_d_mpi -s topol.tpr -cpi state.cpt<br />
<br />
Simulation is completed with warning<br />
<br />
WARNING: The checkpoint state entries do not match the simulation,<br />
see the log file for details<br />
<br />
and Pressure again increases up to 60 bar<br />
<br />
Total Energy Temperature Pressure (bar) Cons. rmsd ()<br />
-1.82304e+04 2.99992e+02 6.20706e+01 0.00000e+00<br />
<br />
<br />
I want to know if this is a right procedure for switching ensemble.<br />
do i need to generate new velocities during second run using NVT ensemble?<br />
If this is correct, how can i reach the target of Pressure 1 bar using this approach?<br />
<br />
I am using following topology file:<br />
Can anyone please tell me if this topology is o.k to use<br />
<br />
<br />
; Include forcefield parameters<br />
#include "ffG53a6.itp"<br />
<br />
[ moleculetype ]<br />
; Name nrexcl<br />
G269 3<br />
[ atoms ]<br />
; nr type resnr resid atom cgnr charge mass total_charge<br />
1 OE 1 G269 O 1 -0.345 15.9994<br />
2 CH2 1 G269 C 1 0.151 14.0270<br />
3 CH2 1 G269 C 1 0.194 14.0270 ; 0.000<br />
4 CH2 1 G269 C 2 0.231 14.0270<br />
5 OA 1 G269 O 2 -0.617 15.9994<br />
6 H 1 G269 H 2 0.386 1.0080 ; 0.000<br />
7 CH2 1 G269 C 3 -0.035 14.0270<br />
8 CH2 1 G269 C 3 0.143 14.0270<br />
9 CH3 1 G269 C 3 -0.108 15.0350 ; -0.000<br />
; total charge of the molecule: 0.000<br />
[ bonds ]<br />
; ai aj funct c0 c1<br />
1 2 2 0.1430 8.1800e+06<br />
1 3 2 0.1430 8.1800e+06<br />
2 4 2 0.1520 5.4300e+06<br />
3 7 2 0.1520 5.4300e+06<br />
4 5 2 0.1430 8.1800e+06<br />
5 6 2 0.1000 2.3200e+07<br />
7 8 2 0.1530 7.1500e+06<br />
8 9 2 0.1530 7.1500e+06<br />
[ pairs ]<br />
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp<br />
1 5 1<br />
1 8 1<br />
2 6 1<br />
2 7 1<br />
3 4 1<br />
3 9 1<br />
[ angles ]<br />
; ai aj ak funct angle fc<br />
2 1 3 2 109.50 380.00<br />
1 2 4 2 109.50 320.00<br />
1 3 7 2 109.50 320.00<br />
2 4 5 2 111.00 530.00<br />
4 5 6 2 108.53 443.00<br />
3 7 8 2 111.00 530.00<br />
7 8 9 2 111.00 530.00<br />
[ dihedrals ]<br />
; GROMOS improper dihedrals<br />
; ai aj ak al funct angle fc<br />
[ dihedrals ]<br />
; ai aj ak al funct ph0 cp mult<br />
3 1 2 4 1 0.00 1.26 3<br />
2 1 3 7 1 0.00 1.26 3<br />
1 2 4 5 1 0.00 2.53 3<br />
1 3 7 8 1 0.00 3.77 3<br />
2 4 5 6 1 0.00 1.26 3<br />
3 7 8 9 1 0.00 3.77 3<br />
[ exclusions ]<br />
; ai aj funct ; GROMOS 1-4 exclusions<br />
<br />
<br />
<br />
<br />
; Include water topology<br />
#include "spce.itp"<br />
[ system ]<br />
; Name<br />
BE in Water<br />
<br />
[ molecules ]<br />
; Compound #mols<br />
G269 20<br />
SOL 480<br />
<br />
Please help me in this regard.<br />
<br />
Thanks and Regards,<br />
Rini<br />
<br />
----------------<br />
Dr. Rini Gupta<br />
Postdoctoral Fellow<br />
University of British Columbia<br />
Vancouver<br />
<br />
<br />
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