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
--
========================================
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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