[gmx-users] zero atoms for FE P

[Justin A. Lemkul]

Moeed wrote:
> 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...
> 

Probably the most important piece of information is your .mdp file, but you 
didn't post it, so please do.

-Justin

> Thanks
> moeed
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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