[gmx-users] energygrp_excl and PME

[Abil Aliev]

Hello, 
 
 I have used mdp file for md runs with 
 
 coulombtype              = Cut-off 
 
 energygrps          =  Protein  SOL Terminal 
 energygrp_excl     = Terminal Terminal Terminal SOL 
 freezegrps          = Terminal 
 freezedim           = Y Y Y 
 
 and had no warning messages on grompp-ing. But, when
I change 
 coulombtype              = PME 
 
 a warning message is issued by grompp: 
 
 "WARNING 1 [file "stide.top", line 40]: 
 Can not exclude the lattice Coulomb energy between
energy groups" 
 
 Is there anyway to avoid this warning by changing
energygrp_excl or other options in the mdp file while
keeping PME? 
 
 Line 40 of stide.top simply says: SOL             
2479 
 
 The full text of the mdp file is attached below. 
 
 Thank you, 
 abil 
 
 ------------------------------------- 
 cpp                 =  /lib/cpp 
 constraints         =  all-bonds 
 integrator          =  md 
 dt                  =  0.002    ; ps ! 
 nsteps              =10000000 
 
 comm-grps           = Protein 
 comm-mode           = Linear 
 nstcomm = 1 
 nstxout = 25 
 nstvout = 1000 
 nstfout = 0 
 nstlog  = 100 
 nstenergy =100 
 nstlist = 5 
 ns_type = grid 
 
 pbc                 = xyz 
 
 rlist               = 0.9 
 coulombtype         = PME 
 rcoulomb            = 0.9 
 
 rvdw                = 1.4 
 
 DispCorr            = Ener 
 
 fourierspacing      = 0.1 
 pme_order           = 4 
 
 ewald_rtol          = 1e-5 
 optimize_fft        = yes 
 
 lincs-iter = 2 
 
 Tcoupl              =  berendsen 
 tc-grps             =  Protein  SOL  Terminal 
 tau_t               =  0.1      0.1   0.1 
 ref_t               =  300      300   300 
 
 Pcoupl              = no 
 
 gen_vel             =  no 
 gen_temp            =  300.0 
 gen_seed            =  173529 
 
 eenergygrps          =  Protein  SOL Terminal 
 nergygrp_excl     = Terminal Terminal Terminal SOL
Terminal Protein 
 freezegrps          = Terminal 
 freezedim           = Y Y Y 


	
	
		
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