[gmx-users] Re: Problems with g_membed tools

[Mark Abraham]

On 11/11/2011 5:13 PM, LindaSong wrote:
> 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 inexper ienced user, I don't know how to improve the 
> mdp file. Can you give me any hint?

Use a text editor that writes plain text. Junk " " throughout 
cannot help things. As before, reporting the actual text of the warning 
is critical to working out what might be wrong.

Mark

> 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&n bsp;
>     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 &nb sp;      = 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 & nbsp;
>     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 &nb sp;         =  Y Y Y
>     ; Energy group exclusions
>     energygrp_excl      =  Protein Protein
>
>
> Thanks a lot!
> Linda
>
>
>
>
>
>
>

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