[gmx-users] Re: Problems with g_membed tools

[Wanling Song]

I used the mdp file listed previously to generate the tpr file. It
gave this warning:


WARNING 1 [file membed.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups


then I ignored the warning with -maxwarn 1 and gave the tpr file to
g_membed, command line like this:


  g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000


Then it seems the g_membed did one iteration and stopped , it returned this:


Back Off! I just backed up step1b.pdb to ./#step1b.pdb.2#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.2#
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program g_membed, VERSION 4.5.3
Source code file: nsgrid.c, line: 540

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


I am wondering if it is because the parameters in the mdp file set
improper. How to change it?

Linda



Does this mean that I need to

2011/11/11 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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 "&nbsp;" 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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