[gmx-users] Re: Problems with g_membed tools

[LindaSong]

Thank you very much for your reply, Mark

It is the topology problem. It seems I did it in a wrong way. Now the topology goes like this:
        [ molecules ]
     ; Compound        #mols
        Protein_chain_A      1
        Protein_chain_A2    1
        POPC                   256
This problem solved.

But then comes a new one. When I did the g_membed, the system blowed up after one iteration!
I think I really shouldn't ignore the warning from the grompp. However, as an inexperienced user, I don't know how to improve the mdp file. Can you give me any hint?
The mdp file for the g_membed is like this:
cpp                 =  /lib/cpp
; Run parameters
integrator      = md          
nsteps          = 1000        
dt              = 0.002       
; Output control
nstxout         = 10          
nstvout         = 10          
nstenergy       = 10       
nstlog          = 10           
; Bond parameters
continuation    = no        
constraint_algorithm = lincs   
constraints     = all-bonds   
lincs_iter      = 1         
lincs_order     = 4            
; Neighborsearching
ns_type         = grid       
nstlist         = 1           
rlist           = 1.4         
rcoulomb        = 1.4        
rvdw            = 1.4        
; Electrostatics
coulombtype     = PME      
pme_order       = 4      
fourierspacing  = 0.16       
; Temperature coupling is on
tcoupl          = V-rescale   
tc-grps         = Protein Non-Protein  
tau_t           = 0.1   0.1    
ref_t           = 300   300   
; Pressure coupling is on
Pcoupl                   = Berendsen
pcoupltype               = semiisotropic
tau_p                    = 1.0
compressibility          = 4.5e-5  4.5e-5
ref_p                    = 1.0   1.0
; Velocity generation
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
; Energy monitoring
energygrps          =  Protein
; Non-equilibrium MD
freezegrps          =  Protein
freezedim           =  Y Y Y
; Energy group exclusions
energygrp_excl      =  Protein Protein


Thanks a lot!
Linda



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111111/a3df9e59/attachment.html>