Hello,
I tried to follow the FE tutorials and get my own system working but it
seems I am missing something coz I get a blank dgdl file. log file is
saying:
There are 0 atoms and 0 charges for free energy perturbation
Removing pbc first time
What I do is running EM (lambda 0) on a solvated system which is already
equilibrated (and density is obtained by NPT) followed by a MD NVT since
density has to be fixed. My guess is I am making mistake in combining itp
file of hexane into polymer (solute).
EM
grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr >&
output.grompp_em
mdrun -s em-l0.tpr -o em-l0.trr -c em-l0.gro -g em-l0.log -e em-l0.edr -v
>& output.mdrun_em
MD
grompp -f md-l0.mdp -c em-l0.gro -p PE60-0c-itp.top -o md-l0.tpr -n
PE-HEX.ndx>& output.grompp_md
mdrun -s md-l0.tpr -o md-l0.trr -c md-l0.gro -g md-l0.log -e md-l0.edr -x
md-l0.xtc -dgdl md-l0.dgdl -v >& output.mdrun_md
PE60-0c-itp.top is:
==========================
; Include forcefield parameters
#include "ffoplsaa.itp"
#include "Hexane-0c.itp"
[ moleculetype ]
; Name nrexcl
Polymer 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_135 1 EthB C1 1 0 12.011 ; qtot
0
2 opls_140 1 EthB H11 1 0 1.008 ; qtot
0
3 opls_140 1 EthB H12 1 0 1.008 ; qtot
0
4 opls_140 1 EthB H13 1 0 1.008 ; qtot
0
5 opls_136 1 EthB C2 2 0 12.011 ; qtot
0
.
.
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Polymer
[ molecules ]
; Compound #mols
Polymer 4
Hexane 480
=======================================
Please help me what wrong is...
Thanks
moeed
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