[gmx-users] zero atoms for FE P

[Moeed]

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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